Starting phenix.real_space_refine on Fri Jul 3 13:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyn_47310/07_2026/9dyn_47310_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyn_47310/07_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_47310/07_2026/9dyn_47310_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyn_47310/07_2026/9dyn_47310_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyn_47310/07_2026/9dyn_47310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyn_47310/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 10 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 5.26, per 1000 atoms: 0.37 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: 1.35 Conformation dependent library (CDL) restraints added in 1.2 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: 0.31 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: 2.58 Time building geometry restraints manager: 1.75 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: 6.430 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:9.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 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/Z covalent geometry : bond 0.00485 / 0.32 (14775) covalent geometry : angle 0.64373 / 0.44 (20045) hydrogen bonds : bond 0.14242 / 9.47 ( 980) hydrogen bonds : angle 5.18660 / 3.79 ( 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 : 0.384 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: 0.5717 time to fit residues: 117.1270 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 : 0.545 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3522 r_free = 0.3522 target = 0.121243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099482 restraints weight = 35881.577| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.25 r_work: 0.3085 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14775 Z= 0.150 Angle : 0.502 5.296 20045 Z= 0.281 Chirality : 0.038 0.163 2170 Planarity : 0.004 0.067 2505 Dihedral : 6.159 56.494 2032 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.37 % Allowed : 15.86 % Favored : 81.78 % 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 : -0.09 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.016 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/Z covalent geometry : bond 0.00304 / 0.15 (14775) covalent geometry : angle 0.50191 / 0.28 (20045) hydrogen bonds : bond 0.05851 / 3.83 ( 980) hydrogen bonds : angle 4.62512 / 3.39 ( 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 187 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.560 Fit side-chains REVERT: A 287 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8273 (t-100) REVERT: E 165 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7165 (mtm-85) REVERT: E 166 GLU cc_start: 0.8053 (mp0) cc_final: 0.7840 (mp0) REVERT: E 172 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7322 (pt0) REVERT: D 172 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7526 (pt0) REVERT: D 203 ASP cc_start: 0.8253 (p0) cc_final: 0.7889 (p0) REVERT: B 165 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7183 (mtm-85) REVERT: B 172 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7413 (pt0) REVERT: C 19 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7900 (pp30) REVERT: C 172 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7455 (pt0) outliers start: 36 outliers final: 10 residues processed: 170 average time/residue: 0.6744 time to fit residues: 125.2673 Evaluate side-chains 157 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 ARG 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: 3.9990 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100458 restraints weight = 28582.902| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.00 r_work: 0.3109 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14775 Z= 0.145 Angle : 0.470 4.922 20045 Z= 0.265 Chirality : 0.037 0.162 2170 Planarity : 0.003 0.030 2505 Dihedral : 4.801 52.489 1975 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.76 % Allowed : 16.05 % Favored : 81.18 % 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: 1.78 (0.19), residues: 1710 helix: 1.66 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.06 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 13 TYR 0.016 0.001 TYR E 97 PHE 0.023 0.002 PHE B 282 TRP 0.011 0.001 TRP C 182 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14775) covalent geometry : angle 0.47033 / 0.26 (20045) hydrogen bonds : bond 0.05638 / 3.69 ( 980) hydrogen bonds : angle 4.56310 / 3.35 ( 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 193 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.530 Fit side-chains REVERT: A 37 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 172 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7423 (pt0) REVERT: E 19 GLN cc_start: 0.8481 (pt0) cc_final: 0.8086 (pp30) REVERT: E 166 GLU cc_start: 0.8047 (mp0) cc_final: 0.7790 (mp0) REVERT: E 172 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7363 (pt0) REVERT: E 197 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7741 (tpm170) REVERT: D 172 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7535 (pt0) REVERT: D 197 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7623 (tpm170) REVERT: D 203 ASP cc_start: 0.8237 (p0) cc_final: 0.7781 (p0) REVERT: B 165 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7246 (mtm-85) REVERT: B 172 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7423 (pt0) REVERT: B 197 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7624 (tpm170) REVERT: B 252 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 13 ARG cc_start: 0.7102 (ptp90) cc_final: 0.6735 (ptp90) REVERT: C 172 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7512 (pt0) REVERT: C 197 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7625 (tpm170) outliers start: 42 outliers final: 9 residues processed: 173 average time/residue: 0.6075 time to fit residues: 114.6871 Evaluate side-chains 161 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 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 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 287 TRP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 37 LEU 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: 0.9990 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100108 restraints weight = 33305.244| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.17 r_work: 0.3098 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1349 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= 0.143 Angle : 0.476 5.671 20045 Z= 0.265 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.033 2505 Dihedral : 4.023 21.234 1965 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.70 % Allowed : 16.25 % 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: 1.65 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.03 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 13 TYR 0.016 0.001 TYR A 97 PHE 0.025 0.002 PHE B 282 TRP 0.010 0.001 TRP C 182 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14775) covalent geometry : angle 0.47609 / 0.26 (20045) hydrogen bonds : bond 0.05556 / 3.64 ( 980) hydrogen bonds : angle 4.51852 / 3.32 ( 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 186 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.588 Fit side-chains REVERT: A 37 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 159 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: A 172 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7415 (pt0) REVERT: A 197 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7680 (tpm170) REVERT: E 19 GLN cc_start: 0.8495 (pt0) cc_final: 0.8086 (pp30) REVERT: E 44 MET cc_start: 0.8925 (mmt) cc_final: 0.8680 (mmt) REVERT: E 165 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: E 172 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7400 (pt0) REVERT: D 172 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7443 (pt0) REVERT: D 197 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7639 (tpm170) REVERT: D 203 ASP cc_start: 0.8225 (p0) cc_final: 0.7739 (p0) REVERT: B 165 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7235 (mtm-85) REVERT: B 172 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7431 (pt0) REVERT: B 197 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7615 (tpm170) REVERT: B 252 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8005 (mt) REVERT: C 19 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7807 (pp30) REVERT: C 172 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7565 (pt0) REVERT: C 197 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7619 (tpm170) outliers start: 41 outliers final: 14 residues processed: 166 average time/residue: 0.6268 time to fit residues: 113.4515 Evaluate side-chains 165 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 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 165 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 TRP 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 71 GLN 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: 3.9990 chunk 123 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099161 restraints weight = 32257.126| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.14 r_work: 0.3088 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14775 Z= 0.164 Angle : 0.501 6.558 20045 Z= 0.277 Chirality : 0.038 0.159 2170 Planarity : 0.004 0.035 2505 Dihedral : 4.092 22.783 1965 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.57 % Allowed : 16.64 % Favored : 80.79 % 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: 1.62 (0.19), residues: 1710 helix: 1.61 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.22 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 13 TYR 0.018 0.002 TYR A 97 PHE 0.026 0.002 PHE B 282 TRP 0.011 0.001 TRP C 182 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14775) covalent geometry : angle 0.50075 / 0.28 (20045) hydrogen bonds : bond 0.05781 / 3.78 ( 980) hydrogen bonds : angle 4.52774 / 3.33 ( 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: 39 poor density : 145 time to evaluate : 0.464 Fit side-chains REVERT: A 37 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 159 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: A 172 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7407 (pt0) REVERT: A 197 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7697 (tpm170) REVERT: E 19 GLN cc_start: 0.8465 (pt0) cc_final: 0.8078 (pp30) REVERT: E 44 MET cc_start: 0.8920 (mmt) cc_final: 0.8666 (mmt) REVERT: E 165 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7231 (mtm-85) REVERT: E 172 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7403 (pt0) REVERT: E 197 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7738 (tpm170) REVERT: D 172 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7479 (pt0) REVERT: D 197 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7625 (tpm170) REVERT: D 203 ASP cc_start: 0.8143 (p0) cc_final: 0.7638 (p0) REVERT: B 165 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7246 (mtm-85) REVERT: B 172 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7535 (pt0) REVERT: B 197 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7607 (tpm170) REVERT: B 252 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 13 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6750 (ptp90) REVERT: C 19 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: C 172 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7525 (pt0) REVERT: C 197 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7617 (tpm170) outliers start: 39 outliers final: 18 residues processed: 165 average time/residue: 0.5891 time to fit residues: 105.8657 Evaluate side-chains 170 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 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 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 TRP 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 235 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097335 restraints weight = 39241.913| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.37 r_work: 0.3052 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14775 Z= 0.188 Angle : 0.522 6.727 20045 Z= 0.288 Chirality : 0.039 0.160 2170 Planarity : 0.004 0.033 2505 Dihedral : 4.196 21.684 1965 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.03 % Allowed : 16.38 % 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: 1.53 (0.19), residues: 1710 helix: 1.54 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.22 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 13 TYR 0.019 0.002 TYR A 97 PHE 0.026 0.002 PHE B 282 TRP 0.012 0.002 TRP C 182 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (14775) covalent geometry : angle 0.52244 / 0.29 (20045) hydrogen bonds : bond 0.06034 / 3.95 ( 980) hydrogen bonds : angle 4.56789 / 3.36 ( 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 188 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.553 Fit side-chains REVERT: A 37 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 159 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: A 172 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7375 (pt0) REVERT: A 197 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7630 (tpm170) REVERT: E 19 GLN cc_start: 0.8364 (pt0) cc_final: 0.7981 (pp30) REVERT: E 165 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7189 (mtm-85) REVERT: E 197 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7625 (tpm170) REVERT: D 172 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7469 (pt0) REVERT: D 197 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7547 (tpm170) REVERT: D 203 ASP cc_start: 0.7984 (p0) cc_final: 0.7462 (p0) REVERT: B 159 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: B 165 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: B 172 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7567 (pt0) REVERT: B 197 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7521 (tpm170) REVERT: C 19 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7747 (pp30) REVERT: C 165 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: C 166 GLU cc_start: 0.7930 (mp0) cc_final: 0.7643 (mp0) REVERT: C 172 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7499 (pt0) REVERT: C 197 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7566 (tpm170) outliers start: 46 outliers final: 23 residues processed: 164 average time/residue: 0.6396 time to fit residues: 114.2315 Evaluate side-chains 172 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain A residue 100 MET 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 A residue 252 LEU 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 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 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 287 TRP 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 71 GLN 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 287 TRP 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: 0.3980 chunk 44 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101196 restraints weight = 31358.998| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3119 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1500 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= 0.132 Angle : 0.474 7.041 20045 Z= 0.262 Chirality : 0.037 0.161 2170 Planarity : 0.003 0.034 2505 Dihedral : 3.984 20.413 1965 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.24 % Allowed : 16.84 % Favored : 80.92 % 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: 1.69 (0.19), residues: 1710 helix: 1.62 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 13 TYR 0.015 0.001 TYR A 97 PHE 0.026 0.002 PHE B 282 TRP 0.011 0.001 TRP E 182 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (14775) covalent geometry : angle 0.47369 / 0.26 (20045) hydrogen bonds : bond 0.05366 / 3.51 ( 980) hydrogen bonds : angle 4.48452 / 3.30 ( 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 178 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.461 Fit side-chains REVERT: A 159 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: A 172 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7410 (pt0) REVERT: A 197 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7708 (tpm170) REVERT: E 19 GLN cc_start: 0.8455 (pt0) cc_final: 0.8049 (pp30) REVERT: E 165 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7220 (mtm-85) REVERT: E 172 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7402 (pt0) REVERT: E 197 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7732 (tpm170) REVERT: D 42 PHE cc_start: 0.8124 (m-80) cc_final: 0.7893 (m-80) REVERT: D 172 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7413 (pt0) REVERT: D 197 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7633 (tpm170) REVERT: D 203 ASP cc_start: 0.8139 (p0) cc_final: 0.7617 (p0) REVERT: B 159 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: B 165 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7223 (mtm-85) REVERT: B 172 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7537 (pt0) REVERT: B 252 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7990 (mt) REVERT: C 13 ARG cc_start: 0.7072 (ptp90) cc_final: 0.6764 (ptp90) REVERT: C 19 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7767 (pp30) REVERT: C 166 GLU cc_start: 0.8040 (mp0) cc_final: 0.7760 (mp0) REVERT: C 172 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7532 (pt0) outliers start: 34 outliers final: 18 residues processed: 161 average time/residue: 0.6337 time to fit residues: 111.5358 Evaluate side-chains 168 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 MET 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 A residue 252 LEU 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 303 ASP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 165 ARG 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 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 235 VAL 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: 0.5980 chunk 154 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101335 restraints weight = 30399.541| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.07 r_work: 0.3123 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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 = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14775 Z= 0.131 Angle : 0.468 7.236 20045 Z= 0.260 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.039 2505 Dihedral : 3.967 19.535 1965 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.37 % Allowed : 16.91 % 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: 1.70 (0.19), residues: 1710 helix: 1.63 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 13 TYR 0.016 0.001 TYR A 97 PHE 0.027 0.002 PHE B 282 TRP 0.011 0.001 TRP B 182 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (14775) covalent geometry : angle 0.46808 / 0.26 (20045) hydrogen bonds : bond 0.05357 / 3.51 ( 980) hydrogen bonds : angle 4.46930 / 3.29 ( 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 177 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.410 Fit side-chains REVERT: A 159 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: A 166 GLU cc_start: 0.8118 (mp0) cc_final: 0.7895 (mp0) REVERT: A 172 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7394 (pt0) REVERT: A 197 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7705 (tpm170) REVERT: E 19 GLN cc_start: 0.8447 (pt0) cc_final: 0.8036 (pp30) REVERT: E 165 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: E 172 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7410 (pt0) REVERT: E 197 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7732 (tpm170) REVERT: D 172 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7366 (pt0) REVERT: D 197 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7629 (tpm170) REVERT: D 203 ASP cc_start: 0.8066 (p0) cc_final: 0.7524 (p0) REVERT: B 159 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: B 165 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7193 (mtm-85) REVERT: B 172 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7588 (pt0) REVERT: B 197 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7606 (tpm170) REVERT: B 252 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7990 (mt) REVERT: C 13 ARG cc_start: 0.7087 (ptp90) cc_final: 0.6757 (ptp90) REVERT: C 19 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7756 (pp30) REVERT: C 166 GLU cc_start: 0.8047 (mp0) cc_final: 0.7771 (mp0) REVERT: C 172 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7543 (pt0) REVERT: C 197 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7646 (tpm170) outliers start: 36 outliers final: 18 residues processed: 162 average time/residue: 0.6230 time to fit residues: 110.2785 Evaluate side-chains 169 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 100 MET 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 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 71 GLN 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 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: 0.7980 chunk 164 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100348 restraints weight = 33874.331| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.18 r_work: 0.3104 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14775 Z= 0.141 Angle : 0.476 7.221 20045 Z= 0.264 Chirality : 0.037 0.160 2170 Planarity : 0.003 0.038 2505 Dihedral : 3.981 18.575 1965 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.43 % Allowed : 17.11 % 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: 1.67 (0.19), residues: 1710 helix: 1.60 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 13 TYR 0.016 0.001 TYR A 97 PHE 0.028 0.002 PHE B 282 TRP 0.013 0.001 TRP A 287 HIS 0.001 0.000 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14775) covalent geometry : angle 0.47637 / 0.26 (20045) hydrogen bonds : bond 0.05456 / 3.58 ( 980) hydrogen bonds : angle 4.48599 / 3.30 ( 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 179 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.406 Fit side-chains REVERT: A 37 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 159 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: A 166 GLU cc_start: 0.8113 (mp0) cc_final: 0.7879 (mp0) REVERT: A 172 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7421 (pt0) REVERT: A 197 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7719 (tpm170) REVERT: E 19 GLN cc_start: 0.8458 (pt0) cc_final: 0.8029 (pp30) REVERT: E 165 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7205 (mtm-85) REVERT: E 172 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7397 (pt0) REVERT: E 197 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7753 (tpm170) REVERT: D 19 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: D 172 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7380 (pt0) REVERT: D 197 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7645 (tpm170) REVERT: D 203 ASP cc_start: 0.8103 (p0) cc_final: 0.7559 (p0) REVERT: D 266 ASP cc_start: 0.7621 (m-30) cc_final: 0.7415 (t0) REVERT: B 159 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: B 165 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7181 (mtm-85) REVERT: B 172 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7531 (pt0) REVERT: B 197 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7605 (tpm170) REVERT: B 252 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7966 (mt) REVERT: C 13 ARG cc_start: 0.7107 (ptp90) cc_final: 0.6749 (ptp90) REVERT: C 19 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7779 (pp30) REVERT: C 166 GLU cc_start: 0.8073 (mp0) cc_final: 0.7802 (mp0) REVERT: C 172 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7536 (pt0) REVERT: C 197 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7659 (tpm170) outliers start: 37 outliers final: 19 residues processed: 161 average time/residue: 0.6251 time to fit residues: 109.3201 Evaluate side-chains 175 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain A residue 100 MET 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 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 287 TRP Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain D residue 19 GLN 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 71 GLN 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 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: 6.9990 chunk 80 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 151 optimal weight: 0.0170 chunk 129 optimal weight: 0.0470 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101098 restraints weight = 39622.760| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.37 r_work: 0.3109 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14775 Z= 0.120 Angle : 0.463 7.693 20045 Z= 0.257 Chirality : 0.036 0.160 2170 Planarity : 0.003 0.049 2505 Dihedral : 3.917 18.184 1965 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.97 % Allowed : 17.63 % Favored : 80.39 % 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: 1.73 (0.20), residues: 1710 helix: 1.65 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.05 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 13 TYR 0.015 0.001 TYR A 97 PHE 0.027 0.002 PHE B 282 TRP 0.013 0.001 TRP A 287 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (14775) covalent geometry : angle 0.46310 / 0.26 (20045) hydrogen bonds : bond 0.05212 / 3.41 ( 980) hydrogen bonds : angle 4.46321 / 3.29 ( 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 176 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.421 Fit side-chains REVERT: A 37 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 159 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7774 (mm-30) REVERT: A 166 GLU cc_start: 0.7961 (mp0) cc_final: 0.7726 (mp0) REVERT: A 172 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7387 (pt0) REVERT: A 197 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7642 (tpm170) REVERT: E 19 GLN cc_start: 0.8364 (pt0) cc_final: 0.7962 (pp30) REVERT: E 44 MET cc_start: 0.8885 (mmt) cc_final: 0.8641 (mmt) REVERT: E 165 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7096 (mtm-85) REVERT: E 172 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7395 (pt0) REVERT: E 197 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7654 (tpm170) REVERT: D 172 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7354 (pt0) REVERT: D 197 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7573 (tpm170) REVERT: D 203 ASP cc_start: 0.7916 (p0) cc_final: 0.7380 (p0) REVERT: B 159 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: B 172 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7512 (pt0) REVERT: B 197 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7530 (tpm170) REVERT: B 252 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7991 (mt) REVERT: C 13 ARG cc_start: 0.7035 (ptp90) cc_final: 0.6688 (ptp90) REVERT: C 19 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7694 (pp30) REVERT: C 166 GLU cc_start: 0.7924 (mp0) cc_final: 0.7670 (mp0) REVERT: C 172 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7509 (pt0) REVERT: C 197 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7592 (tpm170) outliers start: 30 outliers final: 14 residues processed: 161 average time/residue: 0.6149 time to fit residues: 107.8262 Evaluate side-chains 165 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain A residue 100 MET 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 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 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 197 ARG Chi-restraints excluded: chain C residue 235 VAL 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100570 restraints weight = 40006.284| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.39 r_work: 0.3100 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14775 Z= 0.134 Angle : 0.478 7.430 20045 Z= 0.264 Chirality : 0.037 0.160 2170 Planarity : 0.004 0.046 2505 Dihedral : 3.941 21.551 1965 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.71 % Allowed : 18.09 % Favored : 80.20 % 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: 1.73 (0.20), residues: 1710 helix: 1.65 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.04 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 13 TYR 0.016 0.001 TYR A 97 PHE 0.028 0.002 PHE C 282 TRP 0.013 0.001 TRP A 287 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14775) covalent geometry : angle 0.47800 / 0.26 (20045) hydrogen bonds : bond 0.05337 / 3.50 ( 980) hydrogen bonds : angle 4.45827 / 3.28 ( 2845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5020.21 seconds wall clock time: 86 minutes 24.81 seconds (5184.81 seconds total)