Starting phenix.real_space_refine on Mon Mar 11 04:26:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi8_40062/03_2024/8gi8_40062_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.179 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 P 15 5.49 5 S 60 5.16 5 Na 3 4.78 5 C 4884 2.51 5 N 906 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6990 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2330 Unusual residues: {' NA': 1, 'CLR': 3, 'PEE': 5, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 10, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 25} Not linked: pdbres="LEU A 256 " pdbres="RET A 301 " Not linked: pdbres="RET A 301 " pdbres=" NA A 302 " Not linked: pdbres=" NA A 302 " pdbres="CLR A 303 " Not linked: pdbres="CLR A 303 " pdbres="CLR A 304 " Not linked: pdbres="CLR A 304 " pdbres="CLR A 305 " ... (remaining 20 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2330 Unusual residues: {' NA': 1, 'CLR': 3, 'PEE': 5, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 10, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 25} Not linked: pdbres="LEU B 256 " pdbres="RET B 301 " Not linked: pdbres="RET B 301 " pdbres=" NA B 302 " Not linked: pdbres=" NA B 302 " pdbres="CLR B 303 " Not linked: pdbres="CLR B 303 " pdbres="CLR B 304 " Not linked: pdbres="CLR B 304 " pdbres="CLR B 305 " ... (remaining 20 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2330 Unusual residues: {' NA': 1, 'CLR': 3, 'PEE': 5, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 10, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 25} Not linked: pdbres="LEU C 256 " pdbres="RET C 301 " Not linked: pdbres="RET C 301 " pdbres=" NA C 302 " Not linked: pdbres=" NA C 302 " pdbres="CLR C 303 " Not linked: pdbres="CLR C 303 " pdbres="CLR C 304 " Not linked: pdbres="CLR C 304 " pdbres="CLR C 305 " ... (remaining 20 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.34, per 1000 atoms: 0.62 Number of scatterers: 6990 At special positions: 0 Unit cell: (79.31, 77.25, 76.22, 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) S 60 16.00 P 15 15.00 Na 3 11.00 O 1122 8.00 N 906 7.00 C 4884 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 - 3.50 Amino acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 976.5 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 72.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.755A pdb=" N LEU A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.934A pdb=" N SER A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 89 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.709A pdb=" N PHE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 163 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.623A pdb=" N LEU A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 174 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 4.577A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.538A pdb=" N THR A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.756A pdb=" N LEU B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 90 removed outlier: 3.934A pdb=" N SER B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 89 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 126 through 144 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.710A pdb=" N PHE B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 163 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.623A pdb=" N LEU B 167 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 168 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 4.577A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.538A pdb=" N THR B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.756A pdb=" N LEU C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 90 removed outlier: 3.934A pdb=" N SER C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 89 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.710A pdb=" N PHE C 152 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 163 " --> pdb=" O CYS C 160 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.623A pdb=" N LEU C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 168 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 208 removed outlier: 4.577A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 234 through 251 removed outlier: 3.538A pdb=" N THR C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 738 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: 2.06 Time building geometry restraints manager: 3.15 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: 1188 1.33 - 1.45: 1847 1.45 - 1.57: 3988 1.57 - 1.69: 60 1.69 - 1.81: 96 Bond restraints: 7179 Sorted by residual: bond pdb=" O4P PEE B 307 " pdb=" P PEE B 307 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE A 307 " pdb=" P PEE A 307 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" O4P PEE C 307 " pdb=" P PEE C 307 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE C 306 " pdb=" P PEE C 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O4P PEE A 306 " pdb=" P PEE A 306 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.75e+01 ... (remaining 7174 not shown) Histogram of bond angle deviations from ideal: 90.58 - 99.27: 24 99.27 - 107.96: 480 107.96 - 116.65: 4366 116.65 - 125.35: 4550 125.35 - 134.04: 213 Bond angle restraints: 9633 Sorted by residual: angle pdb=" O1P PEE B 308 " pdb=" P PEE B 308 " pdb=" O2P PEE B 308 " ideal model delta sigma weight residual 119.43 133.39 -13.96 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O1P PEE C 308 " pdb=" P PEE C 308 " pdb=" O2P PEE C 308 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE A 308 " pdb=" P PEE A 308 " pdb=" O2P PEE A 308 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE B 307 " pdb=" P PEE B 307 " pdb=" O2P PEE B 307 " ideal model delta sigma weight residual 119.43 133.33 -13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O1P PEE A 307 " pdb=" P PEE A 307 " pdb=" O2P PEE A 307 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 ... (remaining 9628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 4377 34.37 - 68.74: 219 68.74 - 103.11: 30 103.11 - 137.48: 27 137.48 - 171.85: 33 Dihedral angle restraints: 4686 sinusoidal: 2592 harmonic: 2094 Sorted by residual: dihedral pdb=" N PEE C 306 " pdb=" C4 PEE C 306 " pdb=" C5 PEE C 306 " pdb=" O4P PEE C 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.88 -171.85 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE A 306 " pdb=" C4 PEE A 306 " pdb=" C5 PEE A 306 " pdb=" O4P PEE A 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.86 -171.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE B 306 " pdb=" C4 PEE B 306 " pdb=" C5 PEE B 306 " pdb=" O4P PEE B 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.83 -171.80 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 858 0.085 - 0.170: 51 0.170 - 0.256: 9 0.256 - 0.341: 18 0.341 - 0.426: 24 Chirality restraints: 960 Sorted by residual: chirality pdb=" C2 PEE C 307 " pdb=" C1 PEE C 307 " pdb=" C3 PEE C 307 " pdb=" O2 PEE C 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C2 PEE B 307 " pdb=" C1 PEE B 307 " pdb=" C3 PEE B 307 " pdb=" O2 PEE B 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C2 PEE A 307 " pdb=" C1 PEE A 307 " pdb=" C3 PEE A 307 " pdb=" O2 PEE A 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 957 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.24e-01 pdb=" N PRO C 95 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO A 95 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO B 95 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.014 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 63 2.53 - 3.12: 5251 3.12 - 3.71: 10778 3.71 - 4.31: 17054 4.31 - 4.90: 28275 Nonbonded interactions: 61421 Sorted by model distance: nonbonded pdb=" OE2 GLU B 65 " pdb=" N LYS C 126 " model vdw 1.935 2.520 nonbonded pdb=" OE2 GLU A 65 " pdb=" N LYS B 126 " model vdw 1.935 2.520 nonbonded pdb=" N LYS A 126 " pdb=" OE2 GLU C 65 " model vdw 1.936 2.520 nonbonded pdb=" OH TYR A 150 " pdb=" O5 PEE A 308 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR B 150 " pdb=" O5 PEE B 308 " model vdw 2.223 2.440 ... (remaining 61416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 4.060 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.810 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.010 0.125 7179 Z= 0.630 Angle : 1.162 13.963 9633 Z= 0.413 Chirality : 0.088 0.426 960 Planarity : 0.003 0.024 1050 Dihedral : 26.084 171.850 3354 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.34), residues: 714 helix: 1.77 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.14 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 42 HIS 0.002 0.001 HIS A 225 PHE 0.007 0.001 PHE A 152 TYR 0.008 0.001 TYR A 81 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.732 Fit side-chains REVERT: A 21 ASP cc_start: 0.7632 (t70) cc_final: 0.6608 (t70) REVERT: A 81 TYR cc_start: 0.8374 (m-80) cc_final: 0.8137 (m-80) REVERT: A 108 PHE cc_start: 0.8215 (m-80) cc_final: 0.7763 (m-80) REVERT: A 174 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8057 (mtmt) REVERT: A 185 GLN cc_start: 0.8137 (tt0) cc_final: 0.7898 (tt0) REVERT: B 21 ASP cc_start: 0.7347 (t70) cc_final: 0.6580 (t70) REVERT: B 81 TYR cc_start: 0.8411 (m-80) cc_final: 0.8178 (m-80) REVERT: B 106 TYR cc_start: 0.8162 (m-80) cc_final: 0.7787 (m-80) REVERT: B 108 PHE cc_start: 0.8300 (m-80) cc_final: 0.7966 (m-80) REVERT: B 185 GLN cc_start: 0.8117 (tt0) cc_final: 0.7858 (tt0) REVERT: C 21 ASP cc_start: 0.7741 (t70) cc_final: 0.6727 (t70) REVERT: C 106 TYR cc_start: 0.8130 (m-80) cc_final: 0.7734 (m-80) REVERT: C 186 ARG cc_start: 0.7109 (ttt90) cc_final: 0.6858 (ttt90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.9176 time to fit residues: 121.8235 Evaluate side-chains 113 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.1980 chunk 59 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.159 7179 Z= 0.596 Angle : 1.293 19.102 9633 Z= 0.684 Chirality : 0.068 0.819 960 Planarity : 0.018 0.138 1050 Dihedral : 30.920 172.788 2091 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.52 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 8.09 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.32), residues: 714 helix: 0.72 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.03 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.009 TRP B 138 HIS 0.021 0.002 HIS C 125 PHE 0.215 0.007 PHE C 227 TYR 0.231 0.013 TYR B 177 ARG 0.066 0.005 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.686 Fit side-chains REVERT: A 21 ASP cc_start: 0.7659 (t70) cc_final: 0.6585 (t70) REVERT: A 81 TYR cc_start: 0.8085 (m-80) cc_final: 0.7862 (m-80) REVERT: A 108 PHE cc_start: 0.8203 (m-80) cc_final: 0.7723 (m-80) REVERT: A 174 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7829 (mtmt) REVERT: A 185 GLN cc_start: 0.8054 (tt0) cc_final: 0.7835 (tt0) REVERT: B 21 ASP cc_start: 0.7603 (t70) cc_final: 0.6840 (t70) REVERT: B 90 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: B 106 TYR cc_start: 0.8248 (m-80) cc_final: 0.7837 (m-80) REVERT: B 108 PHE cc_start: 0.8312 (m-80) cc_final: 0.7961 (m-80) REVERT: C 21 ASP cc_start: 0.7752 (t70) cc_final: 0.6775 (t70) REVERT: C 106 TYR cc_start: 0.8164 (m-80) cc_final: 0.7804 (m-80) REVERT: C 177 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (t80) outliers start: 8 outliers final: 1 residues processed: 114 average time/residue: 0.9369 time to fit residues: 114.4798 Evaluate side-chains 113 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 177 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 218 GLN C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7179 Z= 0.205 Angle : 0.554 6.042 9633 Z= 0.272 Chirality : 0.039 0.166 960 Planarity : 0.006 0.056 1050 Dihedral : 27.409 179.179 2091 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.96 % Favored : 97.90 % Rotamer: Outliers : 0.97 % Allowed : 9.39 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.32), residues: 714 helix: 1.11 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.004 0.001 HIS C 172 PHE 0.016 0.001 PHE B 134 TYR 0.018 0.002 TYR B 177 ARG 0.006 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.714 Fit side-chains REVERT: A 21 ASP cc_start: 0.7489 (t70) cc_final: 0.6465 (t70) REVERT: A 183 LYS cc_start: 0.7453 (pttt) cc_final: 0.7037 (pptt) REVERT: A 240 MET cc_start: 0.7387 (mmp) cc_final: 0.7126 (mmm) REVERT: B 21 ASP cc_start: 0.7490 (t70) cc_final: 0.6509 (t70) REVERT: B 106 TYR cc_start: 0.8231 (m-80) cc_final: 0.7841 (m-80) REVERT: B 171 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6391 (ttm-80) REVERT: B 183 LYS cc_start: 0.7505 (pttt) cc_final: 0.7232 (pptt) REVERT: C 21 ASP cc_start: 0.7922 (t70) cc_final: 0.7557 (t70) REVERT: C 106 TYR cc_start: 0.8155 (m-80) cc_final: 0.7594 (m-80) REVERT: C 183 LYS cc_start: 0.7322 (pttt) cc_final: 0.7050 (pptt) REVERT: C 229 ASP cc_start: 0.8373 (m-30) cc_final: 0.7898 (m-30) outliers start: 6 outliers final: 2 residues processed: 131 average time/residue: 0.9402 time to fit residues: 131.7579 Evaluate side-chains 117 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.0010 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7179 Z= 0.281 Angle : 0.589 6.013 9633 Z= 0.280 Chirality : 0.041 0.175 960 Planarity : 0.006 0.041 1050 Dihedral : 25.728 179.022 2091 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.29 % Allowed : 11.49 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.32), residues: 714 helix: 0.85 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.02 (0.52), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 42 HIS 0.004 0.001 HIS A 172 PHE 0.015 0.002 PHE B 134 TYR 0.020 0.002 TYR A 177 ARG 0.005 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.773 Fit side-chains REVERT: A 21 ASP cc_start: 0.7515 (t70) cc_final: 0.6444 (t70) REVERT: A 51 MET cc_start: 0.5744 (ttp) cc_final: 0.5484 (ttm) REVERT: A 183 LYS cc_start: 0.7547 (pttt) cc_final: 0.7067 (pptt) REVERT: B 21 ASP cc_start: 0.7527 (t70) cc_final: 0.7278 (t70) REVERT: B 106 TYR cc_start: 0.8285 (m-80) cc_final: 0.7821 (m-80) REVERT: B 171 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6390 (ttm-80) REVERT: B 183 LYS cc_start: 0.7543 (pttt) cc_final: 0.7184 (pptt) REVERT: C 21 ASP cc_start: 0.7918 (t70) cc_final: 0.6692 (t70) REVERT: C 81 TYR cc_start: 0.8037 (m-80) cc_final: 0.7727 (m-80) REVERT: C 106 TYR cc_start: 0.8261 (m-80) cc_final: 0.7776 (m-80) REVERT: C 183 LYS cc_start: 0.7373 (pttt) cc_final: 0.7000 (pptt) REVERT: C 229 ASP cc_start: 0.8385 (m-30) cc_final: 0.8018 (m-30) outliers start: 8 outliers final: 4 residues processed: 123 average time/residue: 0.9399 time to fit residues: 123.7173 Evaluate side-chains 117 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7179 Z= 0.344 Angle : 0.635 7.551 9633 Z= 0.297 Chirality : 0.042 0.176 960 Planarity : 0.006 0.043 1050 Dihedral : 24.806 169.754 2091 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 12.14 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 714 helix: 0.64 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 42 HIS 0.004 0.001 HIS A 172 PHE 0.031 0.002 PHE C 144 TYR 0.020 0.002 TYR B 177 ARG 0.004 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.646 Fit side-chains REVERT: A 21 ASP cc_start: 0.7586 (t70) cc_final: 0.6495 (t70) REVERT: A 51 MET cc_start: 0.5482 (ttp) cc_final: 0.5254 (ttm) REVERT: A 183 LYS cc_start: 0.7571 (pttt) cc_final: 0.7255 (pptt) REVERT: B 21 ASP cc_start: 0.7673 (t70) cc_final: 0.7350 (t70) REVERT: B 106 TYR cc_start: 0.8363 (m-80) cc_final: 0.7775 (m-80) REVERT: B 171 ARG cc_start: 0.7438 (mtm110) cc_final: 0.7218 (mtm110) REVERT: B 183 LYS cc_start: 0.7540 (pttt) cc_final: 0.7187 (pptt) REVERT: C 21 ASP cc_start: 0.7933 (t70) cc_final: 0.7686 (t0) REVERT: C 106 TYR cc_start: 0.8350 (m-80) cc_final: 0.7911 (m-80) REVERT: C 183 LYS cc_start: 0.7518 (pttt) cc_final: 0.7088 (pptt) REVERT: C 229 ASP cc_start: 0.8436 (m-30) cc_final: 0.8132 (m-30) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.9414 time to fit residues: 127.8711 Evaluate side-chains 125 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7179 Z= 0.219 Angle : 0.558 7.349 9633 Z= 0.265 Chirality : 0.039 0.161 960 Planarity : 0.006 0.043 1050 Dihedral : 23.509 177.751 2091 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 12.14 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.32), residues: 714 helix: 0.77 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.87 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 42 HIS 0.003 0.001 HIS C 225 PHE 0.031 0.002 PHE C 144 TYR 0.028 0.002 TYR A 177 ARG 0.005 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.864 Fit side-chains REVERT: A 21 ASP cc_start: 0.7563 (t70) cc_final: 0.6534 (t70) REVERT: A 51 MET cc_start: 0.5566 (ttp) cc_final: 0.5305 (ttm) REVERT: A 171 ARG cc_start: 0.6371 (ttm-80) cc_final: 0.6045 (ttm110) REVERT: A 183 LYS cc_start: 0.7552 (pttt) cc_final: 0.7253 (pptt) REVERT: B 21 ASP cc_start: 0.7631 (t70) cc_final: 0.6696 (t70) REVERT: B 106 TYR cc_start: 0.8299 (m-80) cc_final: 0.7575 (m-80) REVERT: B 171 ARG cc_start: 0.7300 (mtm110) cc_final: 0.6397 (ttm-80) REVERT: B 183 LYS cc_start: 0.7503 (pttt) cc_final: 0.7197 (pptt) REVERT: C 21 ASP cc_start: 0.7873 (t70) cc_final: 0.6866 (t70) REVERT: C 81 TYR cc_start: 0.7943 (m-80) cc_final: 0.7610 (m-80) REVERT: C 106 TYR cc_start: 0.8331 (m-80) cc_final: 0.7704 (m-80) REVERT: C 183 LYS cc_start: 0.7509 (pttt) cc_final: 0.7065 (pptt) REVERT: C 229 ASP cc_start: 0.8403 (m-30) cc_final: 0.7949 (m-30) outliers start: 12 outliers final: 4 residues processed: 132 average time/residue: 0.9710 time to fit residues: 137.2961 Evaluate side-chains 123 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.0020 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.0050 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7179 Z= 0.164 Angle : 0.520 6.661 9633 Z= 0.250 Chirality : 0.037 0.149 960 Planarity : 0.005 0.041 1050 Dihedral : 21.787 174.381 2091 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.65 % Allowed : 13.75 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.32), residues: 714 helix: 0.96 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.70 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS C 225 PHE 0.032 0.001 PHE C 144 TYR 0.013 0.001 TYR A 177 ARG 0.005 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.753 Fit side-chains REVERT: A 21 ASP cc_start: 0.7525 (t70) cc_final: 0.6429 (t70) REVERT: A 51 MET cc_start: 0.5750 (ttp) cc_final: 0.5468 (ttm) REVERT: A 171 ARG cc_start: 0.6190 (ttm-80) cc_final: 0.5879 (ttm110) REVERT: A 183 LYS cc_start: 0.7317 (pttt) cc_final: 0.7113 (pptt) REVERT: B 21 ASP cc_start: 0.7639 (t70) cc_final: 0.6721 (t70) REVERT: B 170 MET cc_start: 0.7303 (mtt) cc_final: 0.7041 (mtt) REVERT: B 171 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6377 (ttm-80) REVERT: B 183 LYS cc_start: 0.7477 (pttt) cc_final: 0.7127 (pptt) REVERT: C 21 ASP cc_start: 0.7844 (t70) cc_final: 0.6884 (t70) REVERT: C 65 GLU cc_start: 0.8353 (tp30) cc_final: 0.7629 (mm-30) REVERT: C 106 TYR cc_start: 0.8246 (m-80) cc_final: 0.7954 (m-80) REVERT: C 183 LYS cc_start: 0.7495 (pttt) cc_final: 0.7097 (pptt) outliers start: 4 outliers final: 0 residues processed: 129 average time/residue: 0.9144 time to fit residues: 126.2590 Evaluate side-chains 121 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7179 Z= 0.300 Angle : 0.624 10.691 9633 Z= 0.292 Chirality : 0.042 0.172 960 Planarity : 0.006 0.043 1050 Dihedral : 21.876 174.128 2091 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.46 % Allowed : 13.59 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 714 helix: 0.78 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 42 HIS 0.003 0.001 HIS B 172 PHE 0.036 0.002 PHE C 144 TYR 0.022 0.002 TYR C 155 ARG 0.003 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.700 Fit side-chains REVERT: A 21 ASP cc_start: 0.7626 (t70) cc_final: 0.6467 (t70) REVERT: A 51 MET cc_start: 0.5578 (ttp) cc_final: 0.5295 (ttm) REVERT: A 183 LYS cc_start: 0.7469 (pttt) cc_final: 0.7199 (pptt) REVERT: B 21 ASP cc_start: 0.7650 (t70) cc_final: 0.6729 (t70) REVERT: B 170 MET cc_start: 0.7310 (mtt) cc_final: 0.7015 (mtt) REVERT: B 171 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6389 (ttm-80) REVERT: B 183 LYS cc_start: 0.7534 (pttt) cc_final: 0.7197 (pptt) REVERT: C 21 ASP cc_start: 0.7900 (t70) cc_final: 0.6906 (t70) REVERT: C 106 TYR cc_start: 0.8433 (m-80) cc_final: 0.7782 (m-80) REVERT: C 183 LYS cc_start: 0.7544 (pttt) cc_final: 0.7085 (pptt) REVERT: C 229 ASP cc_start: 0.8197 (m-30) cc_final: 0.7928 (m-30) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.8838 time to fit residues: 120.6468 Evaluate side-chains 123 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7179 Z= 0.222 Angle : 0.573 9.404 9633 Z= 0.273 Chirality : 0.040 0.157 960 Planarity : 0.006 0.043 1050 Dihedral : 20.859 177.671 2091 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.97 % Allowed : 14.56 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.32), residues: 714 helix: 0.85 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.87 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 42 HIS 0.003 0.001 HIS C 225 PHE 0.033 0.002 PHE C 144 TYR 0.019 0.001 TYR B 177 ARG 0.006 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 0.713 Fit side-chains REVERT: A 21 ASP cc_start: 0.7617 (t70) cc_final: 0.6492 (t70) REVERT: A 51 MET cc_start: 0.5653 (ttp) cc_final: 0.5374 (ttm) REVERT: A 183 LYS cc_start: 0.7455 (pttt) cc_final: 0.7196 (pptt) REVERT: B 21 ASP cc_start: 0.7612 (t70) cc_final: 0.6689 (t70) REVERT: B 170 MET cc_start: 0.7304 (mtt) cc_final: 0.7012 (mtt) REVERT: B 171 ARG cc_start: 0.7281 (mtm110) cc_final: 0.6431 (ttm-80) REVERT: B 183 LYS cc_start: 0.7470 (pttt) cc_final: 0.7102 (pptt) REVERT: C 21 ASP cc_start: 0.7871 (t70) cc_final: 0.6894 (t70) REVERT: C 106 TYR cc_start: 0.8413 (m-80) cc_final: 0.7761 (m-80) REVERT: C 183 LYS cc_start: 0.7629 (pttt) cc_final: 0.7240 (pptt) REVERT: C 229 ASP cc_start: 0.8176 (m-30) cc_final: 0.7843 (m-30) REVERT: C 234 SER cc_start: 0.8757 (t) cc_final: 0.8546 (t) outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.9482 time to fit residues: 122.6649 Evaluate side-chains 124 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7179 Z= 0.205 Angle : 0.564 9.288 9633 Z= 0.270 Chirality : 0.039 0.157 960 Planarity : 0.006 0.042 1050 Dihedral : 19.989 164.163 2091 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.97 % Allowed : 14.08 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.32), residues: 714 helix: 0.87 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.84 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 42 HIS 0.003 0.001 HIS B 172 PHE 0.035 0.002 PHE C 144 TYR 0.013 0.001 TYR C 45 ARG 0.004 0.000 ARG C 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.698 Fit side-chains REVERT: A 21 ASP cc_start: 0.7613 (t70) cc_final: 0.6471 (t70) REVERT: A 51 MET cc_start: 0.5729 (ttp) cc_final: 0.5441 (ttm) REVERT: A 183 LYS cc_start: 0.7470 (pttt) cc_final: 0.7204 (pptt) REVERT: B 21 ASP cc_start: 0.7642 (t70) cc_final: 0.6851 (t70) REVERT: B 170 MET cc_start: 0.7291 (mtt) cc_final: 0.6998 (mtt) REVERT: B 171 ARG cc_start: 0.7278 (mtm110) cc_final: 0.6473 (ttm-80) REVERT: B 183 LYS cc_start: 0.7448 (pttt) cc_final: 0.7089 (pptt) REVERT: C 21 ASP cc_start: 0.7834 (t70) cc_final: 0.6962 (t70) REVERT: C 106 TYR cc_start: 0.8412 (m-80) cc_final: 0.7712 (m-80) REVERT: C 183 LYS cc_start: 0.7626 (pttt) cc_final: 0.7248 (pptt) REVERT: C 229 ASP cc_start: 0.8153 (m-30) cc_final: 0.7838 (m-30) REVERT: C 234 SER cc_start: 0.8668 (t) cc_final: 0.8464 (t) outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.9102 time to fit residues: 122.7293 Evaluate side-chains 125 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 41 optimal weight: 0.0000 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN B 185 GLN C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133030 restraints weight = 7087.084| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.39 r_work: 0.3328 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7179 Z= 0.187 Angle : 0.546 9.036 9633 Z= 0.263 Chirality : 0.039 0.153 960 Planarity : 0.006 0.042 1050 Dihedral : 19.456 152.172 2091 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.81 % Allowed : 14.89 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.32), residues: 714 helix: 0.88 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.74 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 PHE 0.035 0.002 PHE A 144 TYR 0.023 0.001 TYR C 177 ARG 0.004 0.000 ARG C 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2674.79 seconds wall clock time: 48 minutes 27.04 seconds (2907.04 seconds total)