Starting phenix.real_space_refine on Thu Feb 5 01:06:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyn_47310/02_2026/9dyn_47310.map" } resolution = 2.44 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= 0.002 sd= 0.039 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 Cl 1 4.86 5 C 9450 2.51 5 N 2360 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14391 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "E" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "D" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "B" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "C" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CA': 1, ' CL': 1, 'PAB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.71, per 1000 atoms: 0.40 Number of scatterers: 14391 At special positions: 0 Unit cell: (92.008, 91.1865, 109.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 O 2495 8.00 N 2360 7.00 C 9450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.689A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.227A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.689A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.226A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 17 through 21 Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.690A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.227A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.689A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.227A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.689A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.227A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 980 hydrogen bonds defined for protein. 2845 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: 2.48 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2694 1.33 - 1.45: 4080 1.45 - 1.57: 7881 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 14775 Sorted by residual: bond pdb=" CE1 HIS E 267 " pdb=" NE2 HIS E 267 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.36e+01 bond pdb=" CE1 HIS D 267 " pdb=" NE2 HIS D 267 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.32e+01 bond pdb=" CE1 HIS A 267 " pdb=" NE2 HIS A 267 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.31e+01 bond pdb=" CE1 HIS C 267 " pdb=" NE2 HIS C 267 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" C4 PAB C 602 " pdb=" N4 PAB C 602 " ideal model delta sigma weight residual 1.378 1.450 -0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 14770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 19168 1.47 - 2.94: 703 2.94 - 4.42: 138 4.42 - 5.89: 18 5.89 - 7.36: 18 Bond angle restraints: 20045 Sorted by residual: angle pdb=" N ARG C 255 " pdb=" CA ARG C 255 " pdb=" C ARG C 255 " ideal model delta sigma weight residual 113.17 106.02 7.15 1.26e+00 6.30e-01 3.22e+01 angle pdb=" N ARG B 255 " pdb=" CA ARG B 255 " pdb=" C ARG B 255 " ideal model delta sigma weight residual 113.17 106.02 7.15 1.26e+00 6.30e-01 3.22e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.17 106.03 7.14 1.26e+00 6.30e-01 3.21e+01 angle pdb=" N ARG D 255 " pdb=" CA ARG D 255 " pdb=" C ARG D 255 " ideal model delta sigma weight residual 113.17 106.04 7.13 1.26e+00 6.30e-01 3.20e+01 angle pdb=" N ARG E 255 " pdb=" CA ARG E 255 " pdb=" C ARG E 255 " ideal model delta sigma weight residual 113.17 106.07 7.10 1.26e+00 6.30e-01 3.18e+01 ... (remaining 20040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 7272 15.87 - 31.74: 765 31.74 - 47.60: 338 47.60 - 63.47: 125 63.47 - 79.34: 20 Dihedral angle restraints: 8520 sinusoidal: 3390 harmonic: 5130 Sorted by residual: dihedral pdb=" CD ARG D 255 " pdb=" NE ARG D 255 " pdb=" CZ ARG D 255 " pdb=" NH1 ARG D 255 " ideal model delta sinusoidal sigma weight residual 0.00 79.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CD ARG C 255 " pdb=" NE ARG C 255 " pdb=" CZ ARG C 255 " pdb=" NH1 ARG C 255 " ideal model delta sinusoidal sigma weight residual 0.00 79.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CD ARG B 255 " pdb=" NE ARG B 255 " pdb=" CZ ARG B 255 " pdb=" NH1 ARG B 255 " ideal model delta sinusoidal sigma weight residual 0.00 79.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1611 0.039 - 0.078: 393 0.078 - 0.117: 124 0.117 - 0.156: 27 0.156 - 0.195: 15 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA VAL E 273 " pdb=" N VAL E 273 " pdb=" C VAL E 273 " pdb=" CB VAL E 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2167 not shown) Planarity restraints: 2505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 255 " 1.061 9.50e-02 1.11e+02 4.75e-01 1.37e+02 pdb=" NE ARG C 255 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 255 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 255 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 255 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG B 255 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 255 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 255 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 255 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 255 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG A 255 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 255 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 255 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 255 " -0.017 2.00e-02 2.50e+03 ... (remaining 2502 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 180 2.57 - 3.15: 12054 3.15 - 3.73: 24298 3.73 - 4.32: 35681 4.32 - 4.90: 57352 Nonbonded interactions: 129565 Sorted by model distance: nonbonded pdb=" O VAL D 109 " pdb=" OG1 THR D 113 " model vdw 1.985 3.040 nonbonded pdb=" O VAL E 109 " pdb=" OG1 THR E 113 " model vdw 1.985 3.040 nonbonded pdb=" O VAL A 109 " pdb=" OG1 THR A 113 " model vdw 1.985 3.040 nonbonded pdb=" O VAL B 109 " pdb=" OG1 THR B 113 " model vdw 1.985 3.040 nonbonded pdb=" O VAL C 109 " pdb=" OG1 THR C 113 " model vdw 1.985 3.040 ... (remaining 129560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'B' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'C' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'D' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'E' and (resid 2 through 239 or resid 241 through 602)) } 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=0.34 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: 5.280 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 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 0.072 14775 Z= 0.316 Angle : 0.644 7.361 20045 Z= 0.438 Chirality : 0.043 0.195 2170 Planarity : 0.021 0.475 2505 Dihedral : 17.039 79.338 5230 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.63 % Allowed : 16.12 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.19), residues: 1710 helix: 1.77 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.07 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 255 TYR 0.017 0.002 TYR E 97 PHE 0.020 0.002 PHE B 80 TRP 0.009 0.001 TRP D 94 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00485 (14775) covalent geometry : angle 0.64373 (20045) hydrogen bonds : bond 0.14242 ( 980) hydrogen bonds : angle 5.18660 ( 2845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7798 (mmt-90) REVERT: A 287 TRP cc_start: 0.8576 (OUTLIER) cc_final: 0.8283 (m-90) REVERT: E 255 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7369 (mmt-90) REVERT: D 255 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7319 (mmt-90) REVERT: D 265 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8588 (ttmm) REVERT: B 265 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8606 (ttmm) outliers start: 40 outliers final: 27 residues processed: 187 average time/residue: 0.6485 time to fit residues: 132.0484 Evaluate side-chains 170 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 287 TRP Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 318 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS E 115 HIS D 115 HIS B 115 HIS C 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097903 restraints weight = 36219.491| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.26 r_work: 0.3061 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14775 Z= 0.160 Angle : 0.510 5.547 20045 Z= 0.286 Chirality : 0.038 0.163 2170 Planarity : 0.004 0.093 2505 Dihedral : 6.226 56.312 2032 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.70 % Allowed : 15.66 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.19), residues: 1710 helix: 1.59 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.08 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.017 0.001 TYR E 97 PHE 0.021 0.002 PHE C 80 TRP 0.010 0.001 TRP C 182 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00332 (14775) covalent geometry : angle 0.50999 (20045) hydrogen bonds : bond 0.06016 ( 980) hydrogen bonds : angle 4.64740 ( 2845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.394 Fit side-chains REVERT: A 37 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 287 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (m-90) REVERT: E 165 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7230 (mtm-85) REVERT: E 172 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7327 (pt0) REVERT: D 172 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7514 (pt0) REVERT: D 203 ASP cc_start: 0.8265 (p0) cc_final: 0.7892 (p0) REVERT: B 165 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7201 (mtm-85) REVERT: B 172 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7414 (pt0) REVERT: C 19 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7887 (pp30) outliers start: 41 outliers final: 12 residues processed: 172 average time/residue: 0.6031 time to fit residues: 113.2605 Evaluate side-chains 159 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 287 TRP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101179 restraints weight = 28832.518| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.01 r_work: 0.3119 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14775 Z= 0.126 Angle : 0.455 4.921 20045 Z= 0.256 Chirality : 0.036 0.164 2170 Planarity : 0.003 0.033 2505 Dihedral : 5.085 78.897 1977 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.24 % Allowed : 16.45 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.19), residues: 1710 helix: 1.73 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.08 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 13 TYR 0.014 0.001 TYR E 97 PHE 0.023 0.002 PHE B 282 TRP 0.010 0.001 TRP E 33 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00249 (14775) covalent geometry : angle 0.45497 (20045) hydrogen bonds : bond 0.05372 ( 980) hydrogen bonds : angle 4.53889 ( 2845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.565 Fit side-chains REVERT: A 172 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7445 (pt0) REVERT: E 19 GLN cc_start: 0.8472 (pt0) cc_final: 0.8085 (pp30) REVERT: E 44 MET cc_start: 0.8913 (mmt) cc_final: 0.8654 (mmt) REVERT: E 172 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7411 (pt0) REVERT: E 197 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7730 (tpm170) REVERT: D 172 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7470 (pt0) REVERT: D 197 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7645 (tpm170) REVERT: D 203 ASP cc_start: 0.8248 (p0) cc_final: 0.7795 (p0) REVERT: B 165 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7195 (mtm-85) REVERT: B 172 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7432 (pt0) REVERT: B 197 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7674 (tpm170) REVERT: B 252 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 265 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8368 (ttmm) REVERT: C 172 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7472 (pt0) REVERT: C 197 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7647 (tpm170) outliers start: 34 outliers final: 9 residues processed: 169 average time/residue: 0.6489 time to fit residues: 119.3274 Evaluate side-chains 160 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 197 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 100 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098615 restraints weight = 32853.265| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.16 r_work: 0.3077 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14775 Z= 0.165 Angle : 0.492 8.414 20045 Z= 0.272 Chirality : 0.038 0.160 2170 Planarity : 0.003 0.034 2505 Dihedral : 4.628 93.753 1967 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.96 % Allowed : 15.99 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.19), residues: 1710 helix: 1.66 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.05 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 13 TYR 0.018 0.001 TYR A 97 PHE 0.023 0.002 PHE B 282 TRP 0.011 0.001 TRP C 182 HIS 0.001 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00357 (14775) covalent geometry : angle 0.49215 (20045) hydrogen bonds : bond 0.05760 ( 980) hydrogen bonds : angle 4.53653 ( 2845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.569 Fit side-chains REVERT: A 159 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: A 172 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7449 (pt0) REVERT: A 197 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7706 (tpm170) REVERT: E 19 GLN cc_start: 0.8490 (pt0) cc_final: 0.8092 (pp30) REVERT: E 165 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7244 (mtm-85) REVERT: E 172 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7432 (pt0) REVERT: E 197 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7767 (tpm170) REVERT: D 172 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7532 (pt0) REVERT: D 197 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7664 (tpm170) REVERT: D 203 ASP cc_start: 0.8253 (p0) cc_final: 0.7772 (p0) REVERT: B 165 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7258 (mtm-85) REVERT: B 172 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7486 (pt0) REVERT: B 197 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7676 (tpm170) REVERT: B 252 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8045 (mt) REVERT: C 13 ARG cc_start: 0.7121 (ptp90) cc_final: 0.6783 (ptp90) REVERT: C 19 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7866 (pp30) REVERT: C 172 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7468 (pt0) REVERT: C 197 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7670 (tpm170) outliers start: 45 outliers final: 13 residues processed: 165 average time/residue: 0.6793 time to fit residues: 121.5677 Evaluate side-chains 163 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 287 TRP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099476 restraints weight = 32887.379| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.16 r_work: 0.3089 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14775 Z= 0.142 Angle : 0.479 6.670 20045 Z= 0.266 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.030 2505 Dihedral : 4.026 24.268 1965 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.37 % Allowed : 16.78 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.19), residues: 1710 helix: 1.69 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.19 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 13 TYR 0.016 0.001 TYR A 97 PHE 0.024 0.002 PHE B 282 TRP 0.011 0.001 TRP E 182 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00296 (14775) covalent geometry : angle 0.47922 (20045) hydrogen bonds : bond 0.05536 ( 980) hydrogen bonds : angle 4.50274 ( 2845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.446 Fit side-chains REVERT: A 159 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 172 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7439 (pt0) REVERT: A 197 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7708 (tpm170) REVERT: E 19 GLN cc_start: 0.8442 (pt0) cc_final: 0.8051 (pp30) REVERT: E 44 MET cc_start: 0.8934 (mmt) cc_final: 0.8698 (mmt) REVERT: E 165 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7229 (mtm-85) REVERT: E 172 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7391 (pt0) REVERT: D 172 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7481 (pt0) REVERT: D 197 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7637 (tpm170) REVERT: D 203 ASP cc_start: 0.8150 (p0) cc_final: 0.7642 (p0) REVERT: B 159 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: B 165 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7252 (mtm-85) REVERT: B 172 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7444 (pt0) REVERT: B 197 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7616 (tpm170) REVERT: B 252 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7986 (mt) REVERT: C 19 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: C 172 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7519 (pt0) REVERT: C 197 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7626 (tpm170) outliers start: 36 outliers final: 12 residues processed: 167 average time/residue: 0.6061 time to fit residues: 109.9317 Evaluate side-chains 164 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 153 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100154 restraints weight = 39945.811| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.38 r_work: 0.3094 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14775 Z= 0.126 Angle : 0.465 6.669 20045 Z= 0.258 Chirality : 0.037 0.161 2170 Planarity : 0.003 0.031 2505 Dihedral : 3.936 23.300 1965 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.24 % Allowed : 17.04 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.19), residues: 1710 helix: 1.73 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 13 TYR 0.015 0.001 TYR A 97 PHE 0.025 0.002 PHE C 282 TRP 0.010 0.001 TRP D 182 HIS 0.001 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00250 (14775) covalent geometry : angle 0.46491 (20045) hydrogen bonds : bond 0.05263 ( 980) hydrogen bonds : angle 4.44941 ( 2845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.542 Fit side-chains REVERT: A 159 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: A 172 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7380 (pt0) REVERT: A 197 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7598 (tpm170) REVERT: E 19 GLN cc_start: 0.8352 (pt0) cc_final: 0.7977 (pp30) REVERT: E 165 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7118 (mtm-85) REVERT: E 172 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7363 (pt0) REVERT: E 197 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7606 (tpm170) REVERT: D 172 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7321 (pt0) REVERT: D 197 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7535 (tpm170) REVERT: D 203 ASP cc_start: 0.7966 (p0) cc_final: 0.7439 (p0) REVERT: B 159 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: B 165 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7115 (mtm-85) REVERT: B 172 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7455 (pt0) REVERT: B 197 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7514 (tpm170) REVERT: B 252 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 13 ARG cc_start: 0.7028 (ptp90) cc_final: 0.6709 (ptp90) REVERT: C 165 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7468 (mtt-85) REVERT: C 166 GLU cc_start: 0.7923 (mp0) cc_final: 0.7663 (mp0) REVERT: C 172 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7430 (pt0) REVERT: C 197 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7572 (tpm170) outliers start: 34 outliers final: 17 residues processed: 163 average time/residue: 0.6233 time to fit residues: 110.3096 Evaluate side-chains 169 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 168 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101161 restraints weight = 31637.953| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.12 r_work: 0.3117 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14775 Z= 0.127 Angle : 0.468 8.756 20045 Z= 0.259 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.031 2505 Dihedral : 3.906 22.632 1965 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.37 % Allowed : 16.97 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.19), residues: 1710 helix: 1.74 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.05 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.015 0.001 TYR E 97 PHE 0.027 0.002 PHE C 282 TRP 0.010 0.001 TRP B 182 HIS 0.002 0.000 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00253 (14775) covalent geometry : angle 0.46792 (20045) hydrogen bonds : bond 0.05246 ( 980) hydrogen bonds : angle 4.43401 ( 2845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.417 Fit side-chains REVERT: A 37 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 159 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: A 172 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7457 (pt0) REVERT: E 19 GLN cc_start: 0.8433 (pt0) cc_final: 0.8025 (pp30) REVERT: E 44 MET cc_start: 0.8926 (mmt) cc_final: 0.8694 (mmt) REVERT: E 165 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: E 172 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7421 (pt0) REVERT: E 197 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7729 (tpm170) REVERT: D 42 PHE cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: D 166 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7649 (mp0) REVERT: D 172 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7370 (pt0) REVERT: D 197 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7625 (tpm170) REVERT: D 203 ASP cc_start: 0.8155 (p0) cc_final: 0.7631 (p0) REVERT: B 159 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: B 165 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7140 (mtm-85) REVERT: B 172 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7508 (pt0) REVERT: B 197 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7623 (tpm170) REVERT: B 252 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 13 ARG cc_start: 0.7045 (ptp90) cc_final: 0.6692 (ptp90) REVERT: C 19 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: C 166 GLU cc_start: 0.8075 (mp0) cc_final: 0.7832 (mp0) REVERT: C 172 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7476 (pt0) REVERT: C 197 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7667 (tpm170) outliers start: 36 outliers final: 18 residues processed: 165 average time/residue: 0.6198 time to fit residues: 111.5361 Evaluate side-chains 173 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100674 restraints weight = 30516.959| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.08 r_work: 0.3112 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14775 Z= 0.139 Angle : 0.472 8.233 20045 Z= 0.261 Chirality : 0.037 0.159 2170 Planarity : 0.003 0.032 2505 Dihedral : 3.926 20.143 1965 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.37 % Allowed : 16.97 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.19), residues: 1710 helix: 1.72 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.05 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.016 0.001 TYR E 97 PHE 0.026 0.002 PHE B 282 TRP 0.010 0.001 TRP C 182 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00286 (14775) covalent geometry : angle 0.47193 (20045) hydrogen bonds : bond 0.05383 ( 980) hydrogen bonds : angle 4.44445 ( 2845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.424 Fit side-chains REVERT: A 37 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 159 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: A 166 GLU cc_start: 0.8112 (mp0) cc_final: 0.7908 (mp0) REVERT: A 172 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7456 (pt0) REVERT: A 197 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7709 (tpm170) REVERT: E 19 GLN cc_start: 0.8432 (pt0) cc_final: 0.8023 (pp30) REVERT: E 44 MET cc_start: 0.8924 (mmt) cc_final: 0.8680 (mmt) REVERT: E 165 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7197 (mtm-85) REVERT: E 172 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7430 (pt0) REVERT: E 197 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7730 (tpm170) REVERT: D 172 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7368 (pt0) REVERT: D 197 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7618 (tpm170) REVERT: D 203 ASP cc_start: 0.8079 (p0) cc_final: 0.7536 (p0) REVERT: B 165 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7141 (mtm-85) REVERT: B 172 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7518 (pt0) REVERT: B 197 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7617 (tpm170) REVERT: B 252 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7957 (mt) REVERT: C 13 ARG cc_start: 0.7075 (ptp90) cc_final: 0.6699 (ptp90) REVERT: C 19 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7757 (pp30) REVERT: C 166 GLU cc_start: 0.8116 (mp0) cc_final: 0.7867 (mp0) REVERT: C 172 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7488 (pt0) REVERT: C 197 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7683 (tpm170) outliers start: 36 outliers final: 15 residues processed: 166 average time/residue: 0.6416 time to fit residues: 115.7426 Evaluate side-chains 170 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099517 restraints weight = 33907.789| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.19 r_work: 0.3090 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14775 Z= 0.148 Angle : 0.481 7.257 20045 Z= 0.266 Chirality : 0.037 0.159 2170 Planarity : 0.003 0.032 2505 Dihedral : 3.969 18.496 1965 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.11 % Allowed : 17.24 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.19), residues: 1710 helix: 1.72 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.017 0.001 TYR E 97 PHE 0.028 0.002 PHE C 282 TRP 0.013 0.001 TRP A 287 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00309 (14775) covalent geometry : angle 0.48072 (20045) hydrogen bonds : bond 0.05522 ( 980) hydrogen bonds : angle 4.47007 ( 2845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.427 Fit side-chains REVERT: A 37 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 159 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: A 165 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: A 166 GLU cc_start: 0.8132 (mp0) cc_final: 0.7914 (mp0) REVERT: A 172 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7455 (pt0) REVERT: A 197 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7718 (tpm170) REVERT: E 19 GLN cc_start: 0.8433 (pt0) cc_final: 0.8004 (pp30) REVERT: E 165 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7212 (mtm-85) REVERT: E 172 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7427 (pt0) REVERT: E 197 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7734 (tpm170) REVERT: D 172 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7359 (pt0) REVERT: D 197 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7628 (tpm170) REVERT: D 203 ASP cc_start: 0.8108 (p0) cc_final: 0.7566 (p0) REVERT: B 165 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7157 (mtm-85) REVERT: B 172 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7557 (pt0) REVERT: B 197 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7623 (tpm170) REVERT: B 252 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7961 (mt) REVERT: C 13 ARG cc_start: 0.7070 (ptp90) cc_final: 0.6680 (ptp90) REVERT: C 19 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7782 (pp30) REVERT: C 166 GLU cc_start: 0.8113 (mp0) cc_final: 0.7855 (mp0) REVERT: C 172 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7486 (pt0) REVERT: C 197 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7689 (tpm170) outliers start: 32 outliers final: 17 residues processed: 163 average time/residue: 0.6258 time to fit residues: 110.9692 Evaluate side-chains 172 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 287 TRP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099080 restraints weight = 39517.549| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.38 r_work: 0.3077 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14775 Z= 0.146 Angle : 0.483 7.437 20045 Z= 0.267 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.032 2505 Dihedral : 3.974 18.281 1965 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.17 % Allowed : 17.37 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.19), residues: 1710 helix: 1.72 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.017 0.001 TYR E 97 PHE 0.028 0.002 PHE C 282 TRP 0.013 0.001 TRP A 287 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00306 (14775) covalent geometry : angle 0.48283 (20045) hydrogen bonds : bond 0.05509 ( 980) hydrogen bonds : angle 4.47009 ( 2845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.523 Fit side-chains REVERT: A 37 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 159 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: A 165 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7435 (mtm-85) REVERT: A 166 GLU cc_start: 0.8001 (mp0) cc_final: 0.7789 (mp0) REVERT: A 172 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7436 (pt0) REVERT: A 197 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7641 (tpm170) REVERT: E 19 GLN cc_start: 0.8344 (pt0) cc_final: 0.7933 (pp30) REVERT: E 165 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7134 (mtm-85) REVERT: E 172 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7413 (pt0) REVERT: E 197 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7633 (tpm170) REVERT: E 249 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7614 (mt) REVERT: D 19 GLN cc_start: 0.8282 (pt0) cc_final: 0.7886 (pp30) REVERT: D 172 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7304 (pt0) REVERT: D 197 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7559 (tpm170) REVERT: D 203 ASP cc_start: 0.7938 (p0) cc_final: 0.7396 (p0) REVERT: B 165 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7103 (mtm-85) REVERT: B 172 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7541 (pt0) REVERT: B 197 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7535 (tpm170) REVERT: B 252 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7973 (mt) REVERT: C 13 ARG cc_start: 0.7041 (ptp90) cc_final: 0.6656 (ptp90) REVERT: C 19 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7695 (pp30) REVERT: C 100 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8623 (mtp) REVERT: C 165 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: C 166 GLU cc_start: 0.7968 (mp0) cc_final: 0.7722 (mp0) REVERT: C 172 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7454 (pt0) REVERT: C 197 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7611 (tpm170) outliers start: 33 outliers final: 16 residues processed: 163 average time/residue: 0.6184 time to fit residues: 109.8580 Evaluate side-chains 177 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 333 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098980 restraints weight = 39486.619| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.32 r_work: 0.3088 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14775 Z= 0.151 Angle : 0.489 7.900 20045 Z= 0.270 Chirality : 0.038 0.159 2170 Planarity : 0.003 0.033 2505 Dihedral : 3.995 17.535 1965 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.11 % Allowed : 17.30 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.19), residues: 1710 helix: 1.70 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.18 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.017 0.001 TYR A 97 PHE 0.027 0.002 PHE C 282 TRP 0.018 0.001 TRP A 287 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00319 (14775) covalent geometry : angle 0.48908 (20045) hydrogen bonds : bond 0.05581 ( 980) hydrogen bonds : angle 4.48405 ( 2845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5068.59 seconds wall clock time: 87 minutes 5.13 seconds (5225.13 seconds total)