Starting phenix.real_space_refine on Sun Feb 18 03:40:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/02_2024/7zxn_15011_trim_updated.pdb" } resolution = 3.06 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: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 6780 2.51 5 N 1680 2.21 5 O 1638 1.98 5 H 10278 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 178": "OD1" <-> "OD2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20466 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "C" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3383 Classifications: {'peptide': 207} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.09, per 1000 atoms: 0.44 Number of scatterers: 20466 At special positions: 0 Unit cell: (101.37, 102.678, 92.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 1638 8.00 N 1680 7.00 C 6780 6.00 H 10278 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 15.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 6 sheets defined 71.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 156 Processing helix chain 'A' and resid 184 through 219 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 156 Processing helix chain 'B' and resid 184 through 219 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 156 Processing helix chain 'C' and resid 184 through 219 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 156 Processing helix chain 'D' and resid 184 through 219 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 156 Processing helix chain 'E' and resid 184 through 219 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 19 through 42 removed outlier: 4.352A pdb=" N SER F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 156 Processing helix chain 'F' and resid 184 through 219 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= B, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= C, first strand: chain 'C' and resid 165 through 168 Processing sheet with id= D, first strand: chain 'D' and resid 165 through 168 Processing sheet with id= E, first strand: chain 'E' and resid 165 through 168 Processing sheet with id= F, first strand: chain 'F' and resid 165 through 168 738 hydrogen bonds defined for protein. 2196 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: 6.90 Time building geometry restraints manager: 15.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10266 1.03 - 1.23: 191 1.23 - 1.43: 4243 1.43 - 1.63: 5922 1.63 - 1.83: 132 Bond restraints: 20754 Sorted by residual: bond pdb=" CD2 PHE E 180 " pdb=" HD2 PHE E 180 " ideal model delta sigma weight residual 0.930 0.862 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CE1 PHE E 180 " pdb=" HE1 PHE E 180 " ideal model delta sigma weight residual 0.930 0.865 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" ND2 ASN C 54 " pdb="HD22 ASN C 54 " ideal model delta sigma weight residual 0.860 0.924 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" ND2 ASN F 54 " pdb="HD22 ASN F 54 " ideal model delta sigma weight residual 0.860 0.924 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" NH2 ARG A 164 " pdb="HH22 ARG A 164 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.63e+00 ... (remaining 20749 not shown) Histogram of bond angle deviations from ideal: 70.31 - 83.04: 12 83.04 - 95.77: 4 95.77 - 108.51: 6519 108.51 - 121.24: 26985 121.24 - 133.97: 3944 Bond angle restraints: 37464 Sorted by residual: angle pdb=" CZ ARG D 164 " pdb=" NE ARG D 164 " pdb=" HE ARG D 164 " ideal model delta sigma weight residual 117.90 70.31 47.59 3.00e+00 1.11e-01 2.52e+02 angle pdb=" CZ ARG A 164 " pdb=" NE ARG A 164 " pdb=" HE ARG A 164 " ideal model delta sigma weight residual 117.90 70.32 47.58 3.00e+00 1.11e-01 2.52e+02 angle pdb=" CD ARG D 164 " pdb=" NE ARG D 164 " pdb=" HE ARG D 164 " ideal model delta sigma weight residual 117.90 73.17 44.73 3.00e+00 1.11e-01 2.22e+02 angle pdb=" CD ARG A 164 " pdb=" NE ARG A 164 " pdb=" HE ARG A 164 " ideal model delta sigma weight residual 117.90 73.20 44.70 3.00e+00 1.11e-01 2.22e+02 angle pdb=" SD MET E 162 " pdb=" CE MET E 162 " pdb=" HE1 MET E 162 " ideal model delta sigma weight residual 109.00 79.26 29.74 3.00e+00 1.11e-01 9.83e+01 ... (remaining 37459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 9054 14.86 - 29.72: 685 29.72 - 44.58: 194 44.58 - 59.44: 129 59.44 - 74.29: 12 Dihedral angle restraints: 10074 sinusoidal: 5484 harmonic: 4590 Sorted by residual: dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 149.93 -56.93 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 149.92 -56.92 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 149.90 -56.90 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 10071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1539 0.081 - 0.162: 141 0.162 - 0.243: 0 0.243 - 0.324: 18 0.324 - 0.405: 6 Chirality restraints: 1704 Sorted by residual: chirality pdb=" C17 CLR E 501 " pdb=" C13 CLR E 501 " pdb=" C16 CLR E 501 " pdb=" C20 CLR E 501 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C17 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C16 CLR A 501 " pdb=" C20 CLR A 501 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C17 CLR D 501 " pdb=" C13 CLR D 501 " pdb=" C16 CLR D 501 " pdb=" C20 CLR D 501 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 1701 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 164 " -0.593 9.50e-02 1.11e+02 2.00e-01 5.75e+01 pdb=" NE ARG A 164 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 164 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 164 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 164 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG A 164 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 164 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG A 164 " -0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 164 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 164 " 0.593 9.50e-02 1.11e+02 2.00e-01 5.74e+01 pdb=" NE ARG D 164 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG D 164 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG D 164 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 164 " 0.012 2.00e-02 2.50e+03 pdb="HH11 ARG D 164 " -0.011 2.00e-02 2.50e+03 pdb="HH12 ARG D 164 " -0.026 2.00e-02 2.50e+03 pdb="HH21 ARG D 164 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG D 164 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 164 " 0.587 9.50e-02 1.11e+02 1.97e-01 5.35e+01 pdb=" NE ARG E 164 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG E 164 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG E 164 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 164 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 164 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG E 164 " -0.016 2.00e-02 2.50e+03 pdb="HH21 ARG E 164 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG E 164 " -0.003 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1072 2.18 - 2.79: 39890 2.79 - 3.39: 56488 3.39 - 4.00: 69968 4.00 - 4.60: 110370 Nonbonded interactions: 277788 Sorted by model distance: nonbonded pdb=" O ASN D 14 " pdb="HH21 ARG D 22 " model vdw 1.577 1.850 nonbonded pdb=" O ASN B 14 " pdb="HH21 ARG B 22 " model vdw 1.578 1.850 nonbonded pdb=" O ASN A 14 " pdb="HH21 ARG A 22 " model vdw 1.579 1.850 nonbonded pdb=" O ASN E 14 " pdb="HH21 ARG E 22 " model vdw 1.579 1.850 nonbonded pdb=" O ASN C 14 " pdb="HH21 ARG C 22 " model vdw 1.579 1.850 ... (remaining 277783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 0.290 Extract box with map and model: 12.190 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 63.390 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.005 0.059 10476 Z= 0.329 Angle : 0.779 7.367 14304 Z= 0.400 Chirality : 0.056 0.405 1704 Planarity : 0.017 0.270 1674 Dihedral : 12.930 74.294 3978 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.95 (0.23), residues: 1218 helix: 3.06 (0.15), residues: 894 sheet: -1.28 (0.61), residues: 72 loop : -1.39 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.003 0.001 HIS D 123 PHE 0.023 0.003 PHE A 153 TYR 0.008 0.001 TYR B 151 ARG 0.046 0.003 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.6975 (p0) cc_final: 0.6744 (p0) REVERT: C 178 ASP cc_start: 0.6970 (p0) cc_final: 0.6714 (p0) REVERT: D 178 ASP cc_start: 0.6970 (p0) cc_final: 0.6735 (p0) REVERT: F 178 ASP cc_start: 0.6965 (p0) cc_final: 0.6713 (p0) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.4168 time to fit residues: 119.0286 Evaluate side-chains 157 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 0.0970 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN F 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10476 Z= 0.251 Angle : 0.559 4.682 14304 Z= 0.298 Chirality : 0.041 0.180 1704 Planarity : 0.006 0.078 1674 Dihedral : 5.121 41.191 1746 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.08 % Allowed : 10.84 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.78 (0.23), residues: 1218 helix: 3.55 (0.14), residues: 924 sheet: -0.39 (0.63), residues: 72 loop : -1.49 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 44 HIS 0.003 0.001 HIS D 94 PHE 0.018 0.002 PHE F 51 TYR 0.012 0.001 TYR A 151 ARG 0.011 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 213 average time/residue: 0.4911 time to fit residues: 145.9954 Evaluate side-chains 183 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 54 ASN C 54 ASN D 54 ASN E 54 ASN F 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10476 Z= 0.307 Angle : 0.591 3.965 14304 Z= 0.309 Chirality : 0.042 0.149 1704 Planarity : 0.007 0.070 1674 Dihedral : 6.372 58.106 1746 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.69 % Allowed : 11.92 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.32 (0.23), residues: 1218 helix: 3.31 (0.15), residues: 924 sheet: -1.39 (0.54), residues: 102 loop : -1.71 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 24 HIS 0.005 0.001 HIS E 126 PHE 0.019 0.002 PHE D 51 TYR 0.011 0.001 TYR A 151 ARG 0.008 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 1.492 Fit side-chains REVERT: A 47 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: A 57 GLN cc_start: 0.7245 (tt0) cc_final: 0.7014 (tt0) REVERT: B 52 ILE cc_start: 0.8308 (mm) cc_final: 0.8055 (mt) REVERT: B 98 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7278 (tp40) REVERT: D 47 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6308 (pt0) REVERT: D 57 GLN cc_start: 0.7253 (tt0) cc_final: 0.7020 (tt0) REVERT: E 52 ILE cc_start: 0.8306 (mm) cc_final: 0.8057 (mt) REVERT: E 98 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7284 (tp40) outliers start: 30 outliers final: 27 residues processed: 217 average time/residue: 0.4564 time to fit residues: 143.8802 Evaluate side-chains 206 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 80 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10476 Z= 0.215 Angle : 0.502 3.872 14304 Z= 0.260 Chirality : 0.038 0.145 1704 Planarity : 0.005 0.056 1674 Dihedral : 5.632 54.421 1746 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.32 % Allowed : 12.90 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.67 (0.23), residues: 1218 helix: 3.59 (0.15), residues: 924 sheet: -1.34 (0.53), residues: 102 loop : -1.74 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 3 HIS 0.003 0.001 HIS D 94 PHE 0.015 0.002 PHE B 51 TYR 0.010 0.001 TYR D 151 ARG 0.004 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7235 (tt0) cc_final: 0.7017 (tt0) REVERT: B 47 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6261 (pt0) REVERT: B 52 ILE cc_start: 0.8278 (mm) cc_final: 0.8051 (mt) REVERT: C 47 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6212 (pt0) REVERT: C 98 GLN cc_start: 0.7742 (tp40) cc_final: 0.7503 (tp40) REVERT: D 57 GLN cc_start: 0.7244 (tt0) cc_final: 0.7025 (tt0) REVERT: E 47 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6303 (pt0) REVERT: E 52 ILE cc_start: 0.8280 (mm) cc_final: 0.8051 (mt) REVERT: F 47 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6257 (pt0) REVERT: F 98 GLN cc_start: 0.7745 (tp40) cc_final: 0.7507 (tp40) outliers start: 37 outliers final: 27 residues processed: 210 average time/residue: 0.4868 time to fit residues: 145.9715 Evaluate side-chains 212 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.0060 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN D 80 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10476 Z= 0.174 Angle : 0.471 3.897 14304 Z= 0.243 Chirality : 0.037 0.131 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.148 46.586 1746 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.05 % Allowed : 14.34 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.90 (0.23), residues: 1218 helix: 3.78 (0.15), residues: 924 sheet: -1.12 (0.54), residues: 102 loop : -1.88 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 3 HIS 0.002 0.001 HIS A 94 PHE 0.015 0.001 PHE C 51 TYR 0.009 0.001 TYR A 171 ARG 0.003 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6532 (pt0) REVERT: A 57 GLN cc_start: 0.7216 (tt0) cc_final: 0.7002 (tt0) REVERT: A 98 GLN cc_start: 0.7429 (mm110) cc_final: 0.7204 (tp40) REVERT: B 47 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6375 (pt0) REVERT: B 52 ILE cc_start: 0.8233 (mm) cc_final: 0.8022 (mt) REVERT: B 66 ASP cc_start: 0.7863 (m-30) cc_final: 0.7587 (m-30) REVERT: B 98 GLN cc_start: 0.7709 (tp40) cc_final: 0.7336 (mm110) REVERT: C 47 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6263 (pt0) REVERT: C 98 GLN cc_start: 0.7765 (tp40) cc_final: 0.7339 (mm110) REVERT: D 47 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: D 57 GLN cc_start: 0.7225 (tt0) cc_final: 0.7004 (tt0) REVERT: D 98 GLN cc_start: 0.7427 (mm110) cc_final: 0.7210 (tp40) REVERT: E 47 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6412 (pt0) REVERT: E 52 ILE cc_start: 0.8235 (mm) cc_final: 0.8033 (mt) REVERT: E 98 GLN cc_start: 0.7701 (tp40) cc_final: 0.7339 (mm110) REVERT: F 47 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6265 (pt0) REVERT: F 98 GLN cc_start: 0.7770 (tp40) cc_final: 0.7342 (mm110) outliers start: 34 outliers final: 26 residues processed: 208 average time/residue: 0.4558 time to fit residues: 135.9280 Evaluate side-chains 209 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 99 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10476 Z= 0.225 Angle : 0.509 3.931 14304 Z= 0.261 Chirality : 0.038 0.137 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.382 47.997 1746 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.05 % Allowed : 13.44 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.77 (0.23), residues: 1218 helix: 3.66 (0.15), residues: 924 sheet: -1.19 (0.53), residues: 102 loop : -1.72 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 44 HIS 0.003 0.001 HIS D 94 PHE 0.014 0.002 PHE B 51 TYR 0.010 0.001 TYR F 151 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6545 (pt0) REVERT: B 47 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: B 66 ASP cc_start: 0.8013 (m-30) cc_final: 0.7749 (m-30) REVERT: B 98 GLN cc_start: 0.7771 (tp40) cc_final: 0.7372 (mm110) REVERT: C 47 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6206 (pt0) REVERT: C 98 GLN cc_start: 0.7790 (tp40) cc_final: 0.7335 (mm110) REVERT: D 47 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6547 (pt0) REVERT: E 47 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6432 (pt0) REVERT: E 98 GLN cc_start: 0.7767 (tp40) cc_final: 0.7378 (mm110) REVERT: F 47 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6243 (pt0) REVERT: F 98 GLN cc_start: 0.7791 (tp40) cc_final: 0.7336 (mm110) outliers start: 34 outliers final: 26 residues processed: 196 average time/residue: 0.4464 time to fit residues: 129.1445 Evaluate side-chains 208 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10476 Z= 0.151 Angle : 0.454 3.895 14304 Z= 0.232 Chirality : 0.036 0.124 1704 Planarity : 0.004 0.054 1674 Dihedral : 4.646 37.935 1746 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.87 % Allowed : 12.81 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.09 (0.24), residues: 1218 helix: 3.88 (0.15), residues: 924 sheet: -0.96 (0.55), residues: 102 loop : -1.68 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 3 HIS 0.002 0.001 HIS D 94 PHE 0.014 0.001 PHE B 51 TYR 0.008 0.001 TYR D 151 ARG 0.002 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6576 (pt0) REVERT: B 47 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6439 (pt0) REVERT: B 66 ASP cc_start: 0.7935 (m-30) cc_final: 0.7621 (m-30) REVERT: B 98 GLN cc_start: 0.7743 (tp40) cc_final: 0.7295 (mm110) REVERT: C 47 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: C 98 GLN cc_start: 0.7791 (tp40) cc_final: 0.7320 (mm110) REVERT: D 47 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6566 (pt0) REVERT: E 47 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: E 98 GLN cc_start: 0.7742 (tp40) cc_final: 0.7306 (mm110) REVERT: F 47 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6379 (pt0) REVERT: F 98 GLN cc_start: 0.7790 (tp40) cc_final: 0.7317 (mm110) outliers start: 32 outliers final: 19 residues processed: 186 average time/residue: 0.4405 time to fit residues: 122.1304 Evaluate side-chains 187 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10476 Z= 0.256 Angle : 0.515 4.043 14304 Z= 0.263 Chirality : 0.038 0.141 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.394 47.036 1746 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.23 % Allowed : 12.63 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.84 (0.24), residues: 1218 helix: 3.65 (0.15), residues: 924 sheet: -1.08 (0.53), residues: 102 loop : -1.45 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS D 94 PHE 0.013 0.002 PHE F 51 TYR 0.010 0.001 TYR C 151 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6611 (pt0) REVERT: B 47 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6410 (pt0) REVERT: B 66 ASP cc_start: 0.8003 (m-30) cc_final: 0.7759 (m-30) REVERT: B 98 GLN cc_start: 0.7755 (tp40) cc_final: 0.7380 (tp-100) REVERT: C 47 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6344 (pt0) REVERT: C 98 GLN cc_start: 0.7818 (tp40) cc_final: 0.7337 (mm110) REVERT: D 47 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6607 (pt0) REVERT: E 47 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: E 98 GLN cc_start: 0.7749 (tp40) cc_final: 0.7376 (tp-100) REVERT: F 47 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6372 (pt0) REVERT: F 98 GLN cc_start: 0.7816 (tp40) cc_final: 0.7333 (mm110) outliers start: 36 outliers final: 28 residues processed: 183 average time/residue: 0.4655 time to fit residues: 124.0108 Evaluate side-chains 195 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10476 Z= 0.203 Angle : 0.482 3.947 14304 Z= 0.247 Chirality : 0.037 0.130 1704 Planarity : 0.004 0.054 1674 Dihedral : 5.019 42.497 1746 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.32 % Allowed : 12.54 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.89 (0.24), residues: 1218 helix: 3.71 (0.15), residues: 924 sheet: -1.13 (0.53), residues: 102 loop : -1.48 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 24 HIS 0.002 0.001 HIS D 94 PHE 0.013 0.001 PHE F 51 TYR 0.009 0.001 TYR F 151 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6692 (pt0) REVERT: B 47 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: B 66 ASP cc_start: 0.7975 (m-30) cc_final: 0.7724 (m-30) REVERT: B 98 GLN cc_start: 0.7766 (tp40) cc_final: 0.7384 (tp-100) REVERT: C 47 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: C 98 GLN cc_start: 0.7809 (tp40) cc_final: 0.7331 (mm110) REVERT: D 47 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6643 (pt0) REVERT: E 47 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6400 (pt0) REVERT: E 98 GLN cc_start: 0.7762 (tp40) cc_final: 0.7382 (tp-100) REVERT: F 47 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: F 98 GLN cc_start: 0.7808 (tp40) cc_final: 0.7330 (mm110) outliers start: 37 outliers final: 29 residues processed: 173 average time/residue: 0.4539 time to fit residues: 112.9562 Evaluate side-chains 191 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10476 Z= 0.286 Angle : 0.540 4.444 14304 Z= 0.275 Chirality : 0.039 0.149 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.633 50.338 1746 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.32 % Allowed : 12.54 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.78 (0.24), residues: 1218 helix: 3.82 (0.15), residues: 888 sheet: -1.19 (0.52), residues: 102 loop : -1.54 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 44 HIS 0.003 0.001 HIS D 94 PHE 0.014 0.002 PHE F 51 TYR 0.010 0.001 TYR F 151 ARG 0.002 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6707 (pt0) REVERT: B 47 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6390 (pt0) REVERT: B 66 ASP cc_start: 0.8007 (m-30) cc_final: 0.7797 (m-30) REVERT: B 98 GLN cc_start: 0.7766 (tp40) cc_final: 0.7378 (tp-100) REVERT: C 47 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: C 98 GLN cc_start: 0.7813 (tp40) cc_final: 0.7373 (mm110) REVERT: D 47 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: E 47 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6412 (pt0) REVERT: E 98 GLN cc_start: 0.7755 (tp40) cc_final: 0.7372 (tp-100) REVERT: F 47 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6413 (pt0) REVERT: F 98 GLN cc_start: 0.7810 (tp40) cc_final: 0.7369 (mm110) outliers start: 37 outliers final: 28 residues processed: 191 average time/residue: 0.4516 time to fit residues: 124.0861 Evaluate side-chains 208 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101940 restraints weight = 31259.057| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.50 r_work: 0.3014 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10476 Z= 0.150 Angle : 0.444 3.907 14304 Z= 0.228 Chirality : 0.036 0.123 1704 Planarity : 0.004 0.054 1674 Dihedral : 4.500 36.329 1746 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 13.26 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.08 (0.24), residues: 1218 helix: 3.84 (0.15), residues: 924 sheet: -1.14 (0.52), residues: 102 loop : -1.37 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 3 HIS 0.002 0.001 HIS D 94 PHE 0.014 0.001 PHE F 51 TYR 0.007 0.001 TYR A 151 ARG 0.002 0.000 ARG D 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.92 seconds wall clock time: 85 minutes 18.97 seconds (5118.97 seconds total)