Starting phenix.real_space_refine on Wed Nov 20 01:46:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/11_2024/7zxn_15011_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/11_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_15011/11_2024/7zxn_15011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/11_2024/7zxn_15011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/11_2024/7zxn_15011_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxn_15011/11_2024/7zxn_15011_trim.cif" } 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. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.99, per 1000 atoms: 0.54 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 - 3.00 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: 5.65 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 36 helices and 6 sheets defined 76.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 108 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 108 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 108 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 108 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 108 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 18 through 43 removed outlier: 4.352A pdb=" N SER F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 108 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 220 removed outlier: 3.575A pdb=" N LYS F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 810 hydrogen bonds defined for protein. 2394 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: 7.92 Time building geometry restraints manager: 6.57 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: 0.00 - 9.52: 37440 9.52 - 19.04: 4 19.04 - 28.56: 8 28.56 - 38.08: 8 38.08 - 47.59: 4 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: 1048 2.18 - 2.79: 39830 2.79 - 3.39: 56434 3.39 - 4.00: 69860 4.00 - 4.60: 110262 Nonbonded interactions: 277434 Sorted by model distance: nonbonded pdb=" O ASN D 14 " pdb="HH21 ARG D 22 " model vdw 1.577 2.450 nonbonded pdb=" O ASN B 14 " pdb="HH21 ARG B 22 " model vdw 1.578 2.450 nonbonded pdb=" O ASN A 14 " pdb="HH21 ARG A 22 " model vdw 1.579 2.450 nonbonded pdb=" O ASN E 14 " pdb="HH21 ARG E 22 " model vdw 1.579 2.450 nonbonded pdb=" O ASN C 14 " pdb="HH21 ARG C 22 " model vdw 1.579 2.450 ... (remaining 277429 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' } 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: 4.110 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: 0.330 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.180 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.640 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: 0.4467 time to fit residues: 129.7140 Evaluate side-chains 157 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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: 0.7980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 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: 0.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10476 Z= 0.281 Angle : 0.606 4.065 14304 Z= 0.326 Chirality : 0.043 0.186 1704 Planarity : 0.006 0.062 1674 Dihedral : 5.555 48.492 1746 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.08 % Allowed : 10.75 % Favored : 88.17 % 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: 3.88 (0.23), residues: 1218 helix: 3.90 (0.14), residues: 894 sheet: -0.49 (0.62), residues: 72 loop : -1.89 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 44 HIS 0.004 0.001 HIS A 94 PHE 0.018 0.002 PHE F 51 TYR 0.013 0.001 TYR A 151 ARG 0.021 0.001 ARG D 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 204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 198 average time/residue: 0.4956 time to fit residues: 137.8265 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F 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: 0.7980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 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 54 ASN A 80 GLN B 54 ASN B 80 GLN C 54 ASN C 80 GLN D 54 ASN D 80 GLN E 54 ASN E 80 GLN F 54 ASN F 80 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10476 Z= 0.180 Angle : 0.492 3.805 14304 Z= 0.264 Chirality : 0.038 0.125 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.019 47.115 1746 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.70 % Allowed : 12.10 % Favored : 86.20 % 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: 4.30 (0.23), residues: 1218 helix: 3.94 (0.14), residues: 924 sheet: 0.77 (0.63), residues: 60 loop : -1.62 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 3 HIS 0.003 0.001 HIS B 126 PHE 0.019 0.002 PHE E 51 TYR 0.009 0.001 TYR A 151 ARG 0.009 0.001 ARG D 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 222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.6887 (tt0) cc_final: 0.6585 (tt0) REVERT: D 57 GLN cc_start: 0.6890 (tt0) cc_final: 0.6588 (tt0) outliers start: 19 outliers final: 16 residues processed: 214 average time/residue: 0.4591 time to fit residues: 142.7789 Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 99 GLN Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 78 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.8098 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10476 Z= 0.245 Angle : 0.534 3.842 14304 Z= 0.283 Chirality : 0.040 0.151 1704 Planarity : 0.006 0.054 1674 Dihedral : 5.996 52.384 1746 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.51 % Allowed : 12.63 % Favored : 84.86 % 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: 4.22 (0.23), residues: 1218 helix: 4.14 (0.14), residues: 894 sheet: 0.54 (0.64), residues: 60 loop : -1.96 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 44 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.002 PHE B 51 TYR 0.011 0.001 TYR A 151 ARG 0.006 0.001 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 221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7096 (tt0) cc_final: 0.6726 (tt0) REVERT: C 98 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7313 (tp40) REVERT: D 57 GLN cc_start: 0.7103 (tt0) cc_final: 0.6734 (tt0) REVERT: E 98 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7294 (tp40) REVERT: F 98 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7313 (tp40) outliers start: 28 outliers final: 20 residues processed: 207 average time/residue: 0.4363 time to fit residues: 135.9601 Evaluate side-chains 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 99 GLN 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 C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 99 GLN 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 F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 168 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 98 GLN B 54 ASN C 54 ASN D 54 ASN D 98 GLN E 54 ASN F 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10476 Z= 0.275 Angle : 0.550 3.835 14304 Z= 0.291 Chirality : 0.040 0.150 1704 Planarity : 0.006 0.056 1674 Dihedral : 5.963 56.645 1746 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 14.16 % Favored : 82.89 % 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: 3.82 (0.23), residues: 1218 helix: 3.85 (0.14), residues: 894 sheet: -0.39 (0.60), residues: 66 loop : -1.94 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.003 0.001 HIS A 73 PHE 0.015 0.002 PHE A 51 TYR 0.010 0.002 TYR A 151 ARG 0.003 0.000 ARG D 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 217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7738 (tp40) cc_final: 0.7353 (mm110) outliers start: 33 outliers final: 33 residues processed: 198 average time/residue: 0.4100 time to fit residues: 124.0258 Evaluate side-chains 206 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 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 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 GLN 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 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 43 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN E 54 ASN F 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10476 Z= 0.201 Angle : 0.500 3.846 14304 Z= 0.264 Chirality : 0.038 0.134 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.406 49.849 1746 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 13.89 % Favored : 83.15 % 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: 3.98 (0.24), residues: 1218 helix: 4.00 (0.14), residues: 894 sheet: -0.28 (0.59), residues: 66 loop : -2.04 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.002 0.001 HIS B 73 PHE 0.017 0.001 PHE C 51 TYR 0.009 0.001 TYR A 151 ARG 0.002 0.000 ARG A 164 *********************** 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 212 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7726 (tp40) cc_final: 0.7326 (mm110) REVERT: E 98 GLN cc_start: 0.7705 (tp40) cc_final: 0.7333 (mm110) outliers start: 33 outliers final: 26 residues processed: 198 average time/residue: 0.4321 time to fit residues: 128.8095 Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 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 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 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 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN D 98 GLN E 54 ASN F 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10476 Z= 0.195 Angle : 0.493 3.830 14304 Z= 0.260 Chirality : 0.038 0.136 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.193 45.809 1746 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.78 % Allowed : 14.16 % Favored : 83.06 % 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: 4.07 (0.15), residues: 894 sheet: -0.24 (0.59), residues: 66 loop : -1.99 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.003 0.001 HIS D 73 PHE 0.015 0.001 PHE F 51 TYR 0.009 0.001 TYR A 151 ARG 0.003 0.000 ARG F 183 *********************** 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 209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7747 (tp40) cc_final: 0.7294 (mm110) REVERT: E 66 ASP cc_start: 0.8126 (m-30) cc_final: 0.7875 (m-30) REVERT: E 98 GLN cc_start: 0.7722 (tp40) cc_final: 0.7339 (mm110) outliers start: 31 outliers final: 22 residues processed: 193 average time/residue: 0.4554 time to fit residues: 128.6475 Evaluate side-chains 189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL 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 63 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 VAL 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 63 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10476 Z= 0.300 Angle : 0.564 4.047 14304 Z= 0.295 Chirality : 0.040 0.153 1704 Planarity : 0.006 0.056 1674 Dihedral : 5.908 54.084 1746 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 3.78 (0.24), residues: 1218 helix: 3.76 (0.15), residues: 894 sheet: -0.26 (0.58), residues: 66 loop : -1.73 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 24 HIS 0.003 0.001 HIS B 73 PHE 0.014 0.002 PHE F 51 TYR 0.010 0.002 TYR F 151 ARG 0.003 0.000 ARG F 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 to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6411 (pt0) REVERT: E 47 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6332 (pt0) REVERT: E 66 ASP cc_start: 0.8165 (m-30) cc_final: 0.7895 (m-30) outliers start: 34 outliers final: 30 residues processed: 185 average time/residue: 0.4445 time to fit residues: 120.9076 Evaluate side-chains 195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 VAL 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 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 43 VAL 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 C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 84 VAL 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 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5578 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= 0.154 Angle : 0.471 3.803 14304 Z= 0.249 Chirality : 0.037 0.124 1704 Planarity : 0.005 0.056 1674 Dihedral : 4.836 40.183 1746 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 14.87 % Favored : 83.42 % 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: 4.13 (0.24), residues: 1218 helix: 3.83 (0.15), residues: 924 sheet: -0.27 (0.58), residues: 66 loop : -1.48 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 3 HIS 0.002 0.001 HIS C 73 PHE 0.008 0.001 PHE D 51 TYR 0.008 0.001 TYR A 151 ARG 0.002 0.000 ARG F 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 188 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7663 (tp40) cc_final: 0.7344 (mm110) REVERT: E 66 ASP cc_start: 0.8105 (m-30) cc_final: 0.7850 (m-30) REVERT: E 98 GLN cc_start: 0.7661 (tp40) cc_final: 0.7350 (mm110) outliers start: 19 outliers final: 14 residues processed: 180 average time/residue: 0.4304 time to fit residues: 114.2419 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10476 Z= 0.190 Angle : 0.488 3.864 14304 Z= 0.258 Chirality : 0.038 0.135 1704 Planarity : 0.005 0.055 1674 Dihedral : 4.932 40.603 1746 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.25 % Allowed : 15.68 % Favored : 83.06 % 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: 4.17 (0.24), residues: 1218 helix: 4.10 (0.15), residues: 894 sheet: -0.22 (0.58), residues: 66 loop : -1.78 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 24 HIS 0.002 0.001 HIS E 73 PHE 0.007 0.001 PHE E 51 TYR 0.008 0.001 TYR A 151 ARG 0.002 0.000 ARG F 183 ********************** 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 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7667 (tp40) cc_final: 0.7346 (mm110) REVERT: E 66 ASP cc_start: 0.8157 (m-30) cc_final: 0.7879 (m-30) REVERT: E 98 GLN cc_start: 0.7661 (tp40) cc_final: 0.7348 (mm110) outliers start: 14 outliers final: 14 residues processed: 178 average time/residue: 0.4904 time to fit residues: 123.7152 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 214 ILE 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: 0.2980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103163 restraints weight = 30582.778| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.47 r_work: 0.3109 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5725 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= 0.152 Angle : 0.464 3.814 14304 Z= 0.246 Chirality : 0.037 0.125 1704 Planarity : 0.004 0.055 1674 Dihedral : 4.477 33.533 1746 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.43 % Allowed : 15.86 % Favored : 82.71 % 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: 4.27 (0.24), residues: 1218 helix: 3.94 (0.15), residues: 924 sheet: -0.13 (0.57), residues: 66 loop : -1.49 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 24 HIS 0.002 0.001 HIS E 73 PHE 0.016 0.001 PHE E 51 TYR 0.007 0.001 TYR A 151 ARG 0.002 0.000 ARG F 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4816.81 seconds wall clock time: 87 minutes 18.55 seconds (5238.55 seconds total)