Starting phenix.real_space_refine on Thu Mar 5 08:25:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_15011_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_15011_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_15011_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_15011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxn_15011/03_2026/7zxn_15011.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.23, per 1000 atoms: 0.16 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: 1.79 Conformation dependent library (CDL) restraints added in 546.5 milliseconds 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: 0.28 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: 4.20 Time building geometry restraints manager: 2.51 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: 0.03 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: 3.610 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: 0.080 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- 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 10494 Z= 0.236 Angle : 0.794 7.367 14340 Z= 0.406 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.046 0.003 ARG A 164 TYR 0.008 0.001 TYR B 151 PHE 0.023 0.003 PHE A 153 TRP 0.012 0.001 TRP A 77 HIS 0.003 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00504 (10476) covalent geometry : angle 0.77938 (14304) SS BOND : bond 0.00357 ( 18) SS BOND : angle 3.12480 ( 36) hydrogen bonds : bond 0.13235 ( 810) hydrogen bonds : angle 4.82833 ( 2394) *********************** 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 : 0.540 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: 0.1842 time to fit residues: 53.2476 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 : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117785 restraints weight = 30850.480| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.59 r_work: 0.3205 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10494 Z= 0.153 Angle : 0.570 4.301 14340 Z= 0.305 Chirality : 0.041 0.172 1704 Planarity : 0.006 0.054 1674 Dihedral : 4.545 27.124 1746 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.08 % Allowed : 10.30 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.23), residues: 1218 helix: 4.00 (0.14), residues: 894 sheet: -0.23 (0.64), residues: 72 loop : -1.79 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 164 TYR 0.011 0.001 TYR A 151 PHE 0.017 0.002 PHE F 51 TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00348 (10476) covalent geometry : angle 0.56330 (14304) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.81037 ( 36) hydrogen bonds : bond 0.05401 ( 810) hydrogen bonds : angle 3.63346 ( 2394) *********************** 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 200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7448 (tt0) cc_final: 0.7071 (tp30) REVERT: B 102 GLU cc_start: 0.7369 (tt0) cc_final: 0.7014 (tp30) REVERT: C 102 GLU cc_start: 0.7455 (tt0) cc_final: 0.7065 (tp30) REVERT: D 102 GLU cc_start: 0.7473 (tt0) cc_final: 0.7093 (tp30) REVERT: E 102 GLU cc_start: 0.7405 (tt0) cc_final: 0.7023 (tp30) REVERT: F 102 GLU cc_start: 0.7457 (tt0) cc_final: 0.7064 (tp30) outliers start: 12 outliers final: 6 residues processed: 194 average time/residue: 0.1975 time to fit residues: 55.3914 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 25 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107087 restraints weight = 31154.173| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.45 r_work: 0.3005 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10494 Z= 0.206 Angle : 0.600 4.317 14340 Z= 0.320 Chirality : 0.042 0.148 1704 Planarity : 0.007 0.067 1674 Dihedral : 6.270 50.486 1746 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.24 % Allowed : 11.29 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.23), residues: 1218 helix: 3.81 (0.14), residues: 894 sheet: -1.25 (0.58), residues: 72 loop : -1.63 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 164 TYR 0.018 0.002 TYR C 171 PHE 0.019 0.002 PHE A 51 TRP 0.009 0.001 TRP A 44 HIS 0.005 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00483 (10476) covalent geometry : angle 0.59421 (14304) SS BOND : bond 0.00534 ( 18) SS BOND : angle 1.74860 ( 36) hydrogen bonds : bond 0.05715 ( 810) hydrogen bonds : angle 3.61611 ( 2394) *********************** 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 214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.428 Fit side-chains REVERT: A 57 GLN cc_start: 0.7218 (tt0) cc_final: 0.6824 (tt0) REVERT: C 34 MET cc_start: 0.8252 (mmp) cc_final: 0.7938 (mmp) REVERT: D 57 GLN cc_start: 0.7216 (tt0) cc_final: 0.6815 (tt0) REVERT: F 34 MET cc_start: 0.8264 (mmp) cc_final: 0.7960 (mmp) outliers start: 25 outliers final: 17 residues processed: 200 average time/residue: 0.1917 time to fit residues: 56.2782 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 175 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 B 80 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 80 GLN C 98 GLN D 80 GLN D 98 GLN E 54 ASN E 80 GLN E 98 GLN F 80 GLN F 98 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114596 restraints weight = 30748.460| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.40 r_work: 0.2992 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10494 Z= 0.168 Angle : 0.546 3.972 14340 Z= 0.289 Chirality : 0.040 0.153 1704 Planarity : 0.006 0.056 1674 Dihedral : 6.003 59.247 1746 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 12.81 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.81 (0.23), residues: 1218 helix: 3.86 (0.14), residues: 894 sheet: -0.03 (0.60), residues: 60 loop : -2.09 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.010 0.001 TYR A 151 PHE 0.018 0.002 PHE B 51 TRP 0.008 0.001 TRP E 44 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00395 (10476) covalent geometry : angle 0.54199 (14304) SS BOND : bond 0.00415 ( 18) SS BOND : angle 1.47328 ( 36) hydrogen bonds : bond 0.04918 ( 810) hydrogen bonds : angle 3.49276 ( 2394) *********************** 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 233 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 28 residues processed: 217 average time/residue: 0.1745 time to fit residues: 57.1413 Evaluate side-chains 208 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 175 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 98 GLN E 98 GLN F 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102920 restraints weight = 31128.069| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.48 r_work: 0.3069 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10494 Z= 0.145 Angle : 0.514 3.843 14340 Z= 0.271 Chirality : 0.038 0.138 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.608 53.496 1746 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.78 % Allowed : 14.87 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.23), residues: 1218 helix: 3.93 (0.14), residues: 894 sheet: -0.44 (0.60), residues: 66 loop : -2.00 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 164 TYR 0.012 0.001 TYR E 171 PHE 0.016 0.002 PHE C 51 TRP 0.006 0.001 TRP D 44 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00331 (10476) covalent geometry : angle 0.51033 (14304) SS BOND : bond 0.00565 ( 18) SS BOND : angle 1.25012 ( 36) hydrogen bonds : bond 0.04594 ( 810) hydrogen bonds : angle 3.42841 ( 2394) *********************** 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 221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 29 residues processed: 203 average time/residue: 0.1840 time to fit residues: 55.3459 Evaluate side-chains 211 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 175 ASN Chi-restraints excluded: chain B residue 178 ASP 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 178 ASP 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 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 99 GLN Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP 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 175 ASN Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 54 ASN B 98 GLN C 98 GLN D 98 GLN E 54 ASN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099444 restraints weight = 31300.248| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.47 r_work: 0.2949 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10494 Z= 0.192 Angle : 0.563 4.156 14340 Z= 0.295 Chirality : 0.040 0.151 1704 Planarity : 0.006 0.055 1674 Dihedral : 5.905 54.520 1746 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.85 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.24), residues: 1218 helix: 3.73 (0.15), residues: 894 sheet: -1.45 (0.52), residues: 102 loop : -1.95 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.011 0.002 TYR C 157 PHE 0.014 0.002 PHE B 51 TRP 0.008 0.001 TRP F 44 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00457 (10476) covalent geometry : angle 0.56109 (14304) SS BOND : bond 0.00481 ( 18) SS BOND : angle 1.15730 ( 36) hydrogen bonds : bond 0.05059 ( 810) hydrogen bonds : angle 3.49062 ( 2394) *********************** 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 232 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 35 residues processed: 205 average time/residue: 0.1784 time to fit residues: 54.6641 Evaluate side-chains 214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 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 178 ASP 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 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 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 84 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 175 ASN 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 0 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 98 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105320 restraints weight = 31312.201| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.43 r_work: 0.3060 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10494 Z= 0.124 Angle : 0.493 3.832 14340 Z= 0.258 Chirality : 0.038 0.135 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.138 44.781 1746 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.23 % Allowed : 13.17 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.24), residues: 1218 helix: 4.03 (0.15), residues: 894 sheet: -0.33 (0.60), residues: 66 loop : -1.95 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 183 TYR 0.009 0.001 TYR A 151 PHE 0.017 0.001 PHE A 51 TRP 0.006 0.001 TRP B 3 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00275 (10476) covalent geometry : angle 0.48890 (14304) SS BOND : bond 0.00341 ( 18) SS BOND : angle 1.29544 ( 36) hydrogen bonds : bond 0.04222 ( 810) hydrogen bonds : angle 3.38670 ( 2394) *********************** 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 210 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 ASP cc_start: 0.8400 (m-30) cc_final: 0.8175 (m-30) outliers start: 36 outliers final: 31 residues processed: 192 average time/residue: 0.1965 time to fit residues: 54.6958 Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 99 GLN Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 178 ASP 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 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 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 99 GLN Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain F residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 98 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 98 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100755 restraints weight = 31391.085| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.46 r_work: 0.2977 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10494 Z= 0.153 Angle : 0.523 3.893 14340 Z= 0.273 Chirality : 0.038 0.145 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.370 46.790 1746 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.23 % Allowed : 13.08 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.24), residues: 1218 helix: 3.95 (0.15), residues: 894 sheet: -1.10 (0.55), residues: 102 loop : -1.86 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 183 TYR 0.009 0.001 TYR F 151 PHE 0.015 0.001 PHE A 51 TRP 0.007 0.001 TRP E 24 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00356 (10476) covalent geometry : angle 0.51984 (14304) SS BOND : bond 0.00412 ( 18) SS BOND : angle 1.22049 ( 36) hydrogen bonds : bond 0.04552 ( 810) hydrogen bonds : angle 3.41889 ( 2394) *********************** 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: 36 poor density : 165 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 ASP cc_start: 0.8434 (m-30) cc_final: 0.8195 (m-30) outliers start: 36 outliers final: 33 residues processed: 180 average time/residue: 0.2041 time to fit residues: 53.6032 Evaluate side-chains 195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 178 ASP 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 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** ** E 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 = 0.3402 r_free = 0.3402 target = 0.126969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102739 restraints weight = 31267.258| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.46 r_work: 0.3022 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10494 Z= 0.121 Angle : 0.483 3.831 14340 Z= 0.253 Chirality : 0.037 0.133 1704 Planarity : 0.005 0.055 1674 Dihedral : 4.831 39.657 1746 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 13.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.24), residues: 1218 helix: 3.84 (0.15), residues: 924 sheet: -0.23 (0.60), residues: 66 loop : -1.54 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 183 TYR 0.008 0.001 TYR A 151 PHE 0.015 0.001 PHE A 51 TRP 0.006 0.001 TRP F 44 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00270 (10476) covalent geometry : angle 0.48084 (14304) SS BOND : bond 0.00293 ( 18) SS BOND : angle 1.03542 ( 36) hydrogen bonds : bond 0.04096 ( 810) hydrogen bonds : angle 3.33705 ( 2394) *********************** 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 202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 ASP cc_start: 0.8413 (m-30) cc_final: 0.8174 (m-30) REVERT: F 66 ASP cc_start: 0.8026 (m-30) cc_final: 0.7693 (m-30) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.2067 time to fit residues: 55.2718 Evaluate side-chains 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 175 ASN 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 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 175 ASN Chi-restraints excluded: chain E residue 209 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099826 restraints weight = 31507.871| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.48 r_work: 0.3022 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10494 Z= 0.153 Angle : 0.520 3.917 14340 Z= 0.271 Chirality : 0.039 0.146 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.269 44.815 1746 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.24 % Allowed : 13.89 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.24), residues: 1218 helix: 3.97 (0.15), residues: 894 sheet: -0.31 (0.59), residues: 66 loop : -1.71 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 107 TYR 0.009 0.001 TYR F 151 PHE 0.014 0.001 PHE A 51 TRP 0.007 0.001 TRP D 24 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00355 (10476) covalent geometry : angle 0.51760 (14304) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.11846 ( 36) hydrogen bonds : bond 0.04518 ( 810) hydrogen bonds : angle 3.40817 ( 2394) ********************** 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 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 66 ASP cc_start: 0.8437 (m-30) cc_final: 0.8109 (m-30) outliers start: 25 outliers final: 25 residues processed: 172 average time/residue: 0.2160 time to fit residues: 52.9309 Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 175 ASN 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 C residue 178 ASP 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 175 ASN 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 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 98 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105554 restraints weight = 31306.164| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.48 r_work: 0.3103 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10494 Z= 0.104 Angle : 0.462 3.768 14340 Z= 0.243 Chirality : 0.037 0.126 1704 Planarity : 0.004 0.055 1674 Dihedral : 4.471 33.803 1746 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.52 % Allowed : 14.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.24), residues: 1218 helix: 3.92 (0.15), residues: 924 sheet: -0.25 (0.59), residues: 66 loop : -1.38 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 183 TYR 0.007 0.001 TYR A 151 PHE 0.015 0.001 PHE A 51 TRP 0.007 0.001 TRP F 3 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00223 (10476) covalent geometry : angle 0.46053 (14304) SS BOND : bond 0.00251 ( 18) SS BOND : angle 0.91622 ( 36) hydrogen bonds : bond 0.03804 ( 810) hydrogen bonds : angle 3.29100 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.52 seconds wall clock time: 76 minutes 50.85 seconds (4610.85 seconds total)