Starting phenix.real_space_refine on Wed Jun 18 03:41:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_15011_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_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/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_15011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_15011.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_15011_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxn_15011/06_2025/7zxn_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-5710/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: 11.34, per 1000 atoms: 0.55 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: 5.77 Conformation dependent library (CDL) restraints added in 1.6 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: 1.61 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: 7.36 Time building geometry restraints manager: 6.94 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 3.310 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: 0.340 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.670 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13235 ( 810) hydrogen bonds : angle 4.82833 ( 2394) SS BOND : bond 0.00357 ( 18) SS BOND : angle 3.12480 ( 36) covalent geometry : bond 0.00504 (10476) covalent geometry : angle 0.77938 (14304) *********************** 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 : 2.888 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: 0.5254 time to fit residues: 152.2925 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 : 1.839 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.136932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112285 restraints weight = 30833.377| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.58 r_work: 0.3107 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 10494 Z= 0.182 Angle : 0.612 4.065 14340 Z= 0.329 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 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 810) hydrogen bonds : angle 3.67491 ( 2394) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.86734 ( 36) covalent geometry : bond 0.00429 (10476) covalent geometry : angle 0.60561 (14304) *********************** 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 : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7436 (tt0) cc_final: 0.7026 (tp30) REVERT: B 102 GLU cc_start: 0.7384 (tt0) cc_final: 0.6971 (tp30) REVERT: D 102 GLU cc_start: 0.7452 (tt0) cc_final: 0.7049 (tp30) REVERT: E 102 GLU cc_start: 0.7378 (tt0) cc_final: 0.6975 (tp30) outliers start: 12 outliers final: 6 residues processed: 198 average time/residue: 0.6097 time to fit residues: 174.6291 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 : 2.585 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107994 restraints weight = 30652.695| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.54 r_work: 0.3076 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10494 Z= 0.154 Angle : 0.532 3.780 14340 Z= 0.283 Chirality : 0.039 0.135 1704 Planarity : 0.006 0.057 1674 Dihedral : 6.001 51.107 1746 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.79 % Allowed : 11.92 % Favored : 86.29 % 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: 4.07 (0.23), residues: 1218 helix: 3.77 (0.14), residues: 924 sheet: 0.43 (0.63), residues: 60 loop : -1.63 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 24 HIS 0.003 0.001 HIS E 126 PHE 0.020 0.002 PHE E 51 TYR 0.010 0.001 TYR A 151 ARG 0.008 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 810) hydrogen bonds : angle 3.49895 ( 2394) SS BOND : bond 0.00425 ( 18) SS BOND : angle 1.53648 ( 36) covalent geometry : bond 0.00355 (10476) covalent geometry : angle 0.52691 (14304) *********************** 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 219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7063 (tt0) cc_final: 0.6664 (tt0) REVERT: D 57 GLN cc_start: 0.7055 (tt0) cc_final: 0.6650 (tt0) outliers start: 20 outliers final: 16 residues processed: 211 average time/residue: 0.4398 time to fit residues: 137.2044 Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 B residue 175 ASN Chi-restraints excluded: chain C residue 63 VAL 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 63 VAL Chi-restraints excluded: chain E residue 175 ASN 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 74 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 98 GLN B 54 ASN D 98 GLN 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 = 0.3450 r_free = 0.3450 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104313 restraints weight = 31208.118| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.54 r_work: 0.3059 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10494 Z= 0.148 Angle : 0.517 3.848 14340 Z= 0.274 Chirality : 0.039 0.147 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.853 58.040 1746 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.69 % Allowed : 12.28 % Favored : 85.04 % 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 (0.23), residues: 1218 helix: 4.06 (0.14), residues: 894 sheet: 0.35 (0.62), residues: 60 loop : -1.92 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.003 0.001 HIS A 73 PHE 0.017 0.002 PHE B 51 TYR 0.010 0.001 TYR D 151 ARG 0.004 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 810) hydrogen bonds : angle 3.40255 ( 2394) SS BOND : bond 0.00365 ( 18) SS BOND : angle 1.46327 ( 36) covalent geometry : bond 0.00341 (10476) covalent geometry : angle 0.51258 (14304) *********************** 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 226 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.683 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: 0.7181 (tt0) cc_final: 0.6754 (tt0) REVERT: B 98 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7455 (tp40) REVERT: C 98 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7528 (tp40) REVERT: C 105 MET cc_start: 0.6028 (mmm) cc_final: 0.5616 (mtp) REVERT: D 57 GLN cc_start: 0.7188 (tt0) cc_final: 0.6762 (tt0) REVERT: E 98 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7459 (tp40) REVERT: F 98 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7509 (tp40) REVERT: F 105 MET cc_start: 0.6018 (mmm) cc_final: 0.5601 (mtp) outliers start: 30 outliers final: 24 residues processed: 210 average time/residue: 0.3955 time to fit residues: 123.7259 Evaluate side-chains 203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 175 ASN 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 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 175 ASN 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 80 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN D 54 ASN E 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102294 restraints weight = 31287.271| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.46 r_work: 0.2974 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10494 Z= 0.163 Angle : 0.529 3.829 14340 Z= 0.279 Chirality : 0.039 0.143 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.764 54.320 1746 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.67 % Allowed : 13.71 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.23), residues: 1218 helix: 3.92 (0.14), residues: 894 sheet: 0.42 (0.62), residues: 60 loop : -2.01 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 44 HIS 0.003 0.001 HIS D 73 PHE 0.015 0.002 PHE F 51 TYR 0.010 0.002 TYR D 151 ARG 0.003 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 810) hydrogen bonds : angle 3.43541 ( 2394) SS BOND : bond 0.00685 ( 18) SS BOND : angle 1.36675 ( 36) covalent geometry : bond 0.00378 (10476) covalent geometry : angle 0.52548 (14304) *********************** 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 228 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7380 (tp40) REVERT: C 105 MET cc_start: 0.5766 (mmm) cc_final: 0.5377 (mtp) REVERT: D 57 GLN cc_start: 0.7237 (tt0) cc_final: 0.6936 (tt0) REVERT: E 98 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7385 (tp40) REVERT: F 105 MET cc_start: 0.5767 (mmm) cc_final: 0.5376 (mtp) outliers start: 41 outliers final: 36 residues processed: 206 average time/residue: 0.4119 time to fit residues: 125.8137 Evaluate side-chains 214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 78 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 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 78 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103232 restraints weight = 31379.440| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.49 r_work: 0.3044 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10494 Z= 0.128 Angle : 0.488 3.870 14340 Z= 0.257 Chirality : 0.038 0.131 1704 Planarity : 0.005 0.054 1674 Dihedral : 5.178 45.899 1746 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.23 % Allowed : 13.89 % 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: 4.05 (0.24), residues: 1218 helix: 4.05 (0.14), residues: 894 sheet: -0.27 (0.60), residues: 66 loop : -1.97 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 3 HIS 0.002 0.001 HIS D 73 PHE 0.016 0.001 PHE C 51 TYR 0.009 0.001 TYR D 151 ARG 0.009 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 810) hydrogen bonds : angle 3.34467 ( 2394) SS BOND : bond 0.00403 ( 18) SS BOND : angle 1.25282 ( 36) covalent geometry : bond 0.00287 (10476) covalent geometry : angle 0.48503 (14304) *********************** 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 219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.532 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: 0.7912 (mm-40) cc_final: 0.7460 (tp40) REVERT: C 105 MET cc_start: 0.5829 (mmm) cc_final: 0.5462 (mtp) REVERT: E 98 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7444 (tp40) REVERT: F 105 MET cc_start: 0.5823 (mmm) cc_final: 0.5460 (mtp) outliers start: 36 outliers final: 25 residues processed: 205 average time/residue: 0.4201 time to fit residues: 125.5369 Evaluate side-chains 195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 78 SER 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 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 D residue 43 VAL 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 54 ASN C 98 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN F 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101458 restraints weight = 31100.249| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.46 r_work: 0.2956 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10494 Z= 0.139 Angle : 0.500 3.829 14340 Z= 0.263 Chirality : 0.038 0.135 1704 Planarity : 0.005 0.057 1674 Dihedral : 5.192 44.721 1746 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 14.16 % Favored : 83.33 % 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 (0.23), residues: 1218 helix: 4.05 (0.14), residues: 894 sheet: -0.23 (0.59), residues: 66 loop : -1.90 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 44 HIS 0.003 0.001 HIS B 73 PHE 0.015 0.001 PHE C 51 TYR 0.011 0.001 TYR D 171 ARG 0.005 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 810) hydrogen bonds : angle 3.34333 ( 2394) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.14750 ( 36) covalent geometry : bond 0.00316 (10476) covalent geometry : angle 0.49722 (14304) *********************** 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 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.737 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: 0.7844 (mm-40) cc_final: 0.7376 (tp40) REVERT: C 105 MET cc_start: 0.5770 (mmm) cc_final: 0.5403 (mtp) REVERT: E 98 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7377 (tp40) REVERT: F 105 MET cc_start: 0.5776 (mmm) cc_final: 0.5417 (mtp) outliers start: 28 outliers final: 25 residues processed: 181 average time/residue: 0.4538 time to fit residues: 120.9964 Evaluate side-chains 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 54 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.125079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100671 restraints weight = 31265.276| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.46 r_work: 0.3036 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10494 Z= 0.142 Angle : 0.505 3.900 14340 Z= 0.264 Chirality : 0.038 0.133 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.171 43.197 1746 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 13.44 % 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 (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: 4.00 (0.15), residues: 894 sheet: -0.15 (0.59), residues: 66 loop : -1.74 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 44 HIS 0.003 0.001 HIS B 73 PHE 0.015 0.001 PHE F 51 TYR 0.013 0.001 TYR D 171 ARG 0.005 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 810) hydrogen bonds : angle 3.36238 ( 2394) SS BOND : bond 0.00378 ( 18) SS BOND : angle 1.07831 ( 36) covalent geometry : bond 0.00326 (10476) covalent geometry : angle 0.50290 (14304) *********************** 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 202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 MET cc_start: 0.5817 (mmm) cc_final: 0.5455 (mtp) REVERT: F 105 MET cc_start: 0.5802 (mmm) cc_final: 0.5457 (mtp) outliers start: 33 outliers final: 26 residues processed: 183 average time/residue: 0.4612 time to fit residues: 120.7127 Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.125872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101510 restraints weight = 31166.215| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.46 r_work: 0.3063 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10494 Z= 0.134 Angle : 0.495 3.860 14340 Z= 0.259 Chirality : 0.038 0.141 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.019 41.562 1746 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 14.25 % Favored : 83.24 % 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: 4.15 (0.24), residues: 1218 helix: 4.06 (0.15), residues: 894 sheet: -0.17 (0.59), residues: 66 loop : -1.68 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 44 HIS 0.003 0.001 HIS E 73 PHE 0.014 0.001 PHE C 51 TYR 0.013 0.001 TYR D 171 ARG 0.003 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 810) hydrogen bonds : angle 3.34716 ( 2394) SS BOND : bond 0.00329 ( 18) SS BOND : angle 1.01444 ( 36) covalent geometry : bond 0.00304 (10476) covalent geometry : angle 0.49260 (14304) *********************** 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 201 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.613 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: 0.7913 (mm-40) cc_final: 0.7455 (tp40) REVERT: C 105 MET cc_start: 0.5817 (mmm) cc_final: 0.5460 (mtp) REVERT: E 66 ASP cc_start: 0.8365 (m-30) cc_final: 0.8118 (m-30) REVERT: E 98 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7453 (tp40) REVERT: F 105 MET cc_start: 0.5799 (mmm) cc_final: 0.5474 (mtp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4932 time to fit residues: 129.8212 Evaluate side-chains 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 175 ASN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100760 restraints weight = 31169.994| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.45 r_work: 0.3029 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5628 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= 0.146 Angle : 0.508 3.922 14340 Z= 0.266 Chirality : 0.038 0.143 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.160 42.061 1746 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 14.78 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.24), residues: 1218 helix: 3.99 (0.15), residues: 894 sheet: -0.07 (0.59), residues: 66 loop : -1.67 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 24 HIS 0.003 0.001 HIS E 73 PHE 0.015 0.001 PHE F 51 TYR 0.013 0.001 TYR D 171 ARG 0.003 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 810) hydrogen bonds : angle 3.37956 ( 2394) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.01474 ( 36) covalent geometry : bond 0.00337 (10476) covalent geometry : angle 0.50596 (14304) ********************** 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 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 MET cc_start: 0.5810 (mmm) cc_final: 0.5462 (mtp) REVERT: E 66 ASP cc_start: 0.8385 (m-30) cc_final: 0.8130 (m-30) REVERT: F 105 MET cc_start: 0.5809 (mmm) cc_final: 0.5475 (mtp) outliers start: 27 outliers final: 27 residues processed: 177 average time/residue: 0.5067 time to fit residues: 125.6914 Evaluate side-chains 187 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 175 ASN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.126775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102021 restraints weight = 31335.316| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.45 r_work: 0.3005 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10494 Z= 0.156 Angle : 0.518 3.923 14340 Z= 0.271 Chirality : 0.039 0.148 1704 Planarity : 0.005 0.055 1674 Dihedral : 5.308 44.733 1746 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.51 % Allowed : 14.78 % 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: 4.01 (0.24), residues: 1218 helix: 3.92 (0.15), residues: 894 sheet: -0.01 (0.60), residues: 66 loop : -1.65 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS E 73 PHE 0.014 0.002 PHE F 51 TYR 0.013 0.001 TYR A 171 ARG 0.003 0.000 ARG F 183 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 810) hydrogen bonds : angle 3.42953 ( 2394) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.02824 ( 36) covalent geometry : bond 0.00361 (10476) covalent geometry : angle 0.51616 (14304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10006.81 seconds wall clock time: 172 minutes 21.78 seconds (10341.78 seconds total)