Starting phenix.real_space_refine on Tue Aug 4 23:32:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2026/8gi8_40062.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.179 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1955 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 375 Unusual residues: {' NA': 1, 'CLR': 3, 'PEE': 5, 'RET': 1} Classifications: {'undetermined': 10, 'water': 15} Link IDs: {None: 24} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: B, C Time building chain proxies: 1.62, per 1000 atoms: 0.23 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 - 3.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 363.9 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... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 150 through 178 Proline residue: A 164 - end of helix removed outlier: 3.576A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 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) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 150 through 178 Proline residue: B 164 - end of helix removed outlier: 3.576A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 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) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 109 through 121 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 150 through 178 Proline residue: C 164 - end of helix removed outlier: 3.576A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 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) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1197 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: 1.21 Time building geometry restraints manager: 0.68 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: 0.00 - 2.79: 9275 2.79 - 5.59: 251 5.59 - 8.38: 92 8.38 - 11.17: 0 11.17 - 13.96: 15 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 119.43 133.35 -13.92 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: 3795 34.37 - 68.74: 198 68.74 - 103.11: 12 103.11 - 137.48: 15 137.48 - 171.85: 12 Dihedral angle restraints: 4032 sinusoidal: 1938 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 4029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 859 0.085 - 0.170: 50 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: 60 2.53 - 3.12: 5155 3.12 - 3.71: 10808 3.71 - 4.31: 16937 4.31 - 4.90: 28257 Nonbonded interactions: 61217 Sorted by model distance: nonbonded pdb=" OE2 GLU B 65 " pdb=" N LYS C 126 " model vdw 1.935 3.120 nonbonded pdb=" OE2 GLU A 65 " pdb=" N LYS B 126 " model vdw 1.935 3.120 nonbonded pdb=" N LYS A 126 " pdb=" OE2 GLU C 65 " model vdw 1.935 3.120 nonbonded pdb=" OH TYR A 150 " pdb=" O5 PEE A 308 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR B 150 " pdb=" O5 PEE B 308 " model vdw 2.223 3.040 ... (remaining 61212 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: 0.02 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: 1.400 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.012 0.362 7185 Z= 0.890 Angle : 1.162 13.963 9633 Z= 0.413 Chirality : 0.088 0.426 960 Planarity : 0.003 0.024 1050 Dihedral : 22.565 171.850 2700 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.22 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 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: 1.50 (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 ARG 0.002 0.000 ARG B 244 TYR 0.008 0.001 TYR A 81 PHE 0.007 0.001 PHE A 152 TRP 0.006 0.001 TRP A 42 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.49 ( 7179) covalent geometry : angle 1.16208 / 0.41 ( 9633) hydrogen bonds : bond 0.22031 / 15.09 ( 405) hydrogen bonds : angle 7.17232 / 5.04 ( 1197) Misc. bond : bond 0.25634 / 12.07 ( 6) *********************** 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 to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.226 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: 0.7786 (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: 0.4124 time to fit residues: 54.7052 Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN C 185 GLN C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125775 restraints weight = 7196.454| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.44 r_work: 0.3187 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7185 Z= 0.151 Angle : 0.562 7.931 9633 Z= 0.268 Chirality : 0.040 0.112 960 Planarity : 0.005 0.035 1050 Dihedral : 25.918 170.208 1437 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.62 % Allowed : 7.61 % Favored : 90.78 % 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: 1.82 (0.33), residues: 714 helix: 1.87 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -0.75 (0.54), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 171 TYR 0.019 0.002 TYR C 177 PHE 0.015 0.002 PHE B 134 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7179) covalent geometry : angle 0.56169 / 0.27 ( 9633) hydrogen bonds : bond 0.04657 / 3.12 ( 405) hydrogen bonds : angle 4.42939 / 3.18 ( 1197) Misc. bond : bond 0.00043 / 0.03 ( 6) *********************** 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 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.220 Fit side-chains REVERT: A 21 ASP cc_start: 0.7851 (t70) cc_final: 0.6859 (t70) REVERT: A 174 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8042 (mtmt) REVERT: A 183 LYS cc_start: 0.7633 (pttt) cc_final: 0.7428 (pptt) REVERT: B 65 GLU cc_start: 0.8198 (tp30) cc_final: 0.7618 (mm-30) REVERT: B 106 TYR cc_start: 0.8350 (m-80) cc_final: 0.8058 (m-80) REVERT: B 183 LYS cc_start: 0.7710 (pttt) cc_final: 0.7406 (pptt) REVERT: B 185 GLN cc_start: 0.8420 (tt0) cc_final: 0.8169 (tt0) REVERT: C 21 ASP cc_start: 0.8081 (t70) cc_final: 0.7876 (t0) REVERT: C 106 TYR cc_start: 0.8325 (m-80) cc_final: 0.8007 (m-80) REVERT: C 183 LYS cc_start: 0.7561 (pttt) cc_final: 0.7205 (pptt) REVERT: C 229 ASP cc_start: 0.8337 (m-30) cc_final: 0.7969 (m-30) outliers start: 10 outliers final: 2 residues processed: 128 average time/residue: 0.4040 time to fit residues: 55.2854 Evaluate side-chains 112 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 125 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125103 restraints weight = 7107.176| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.43 r_work: 0.3248 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7185 Z= 0.150 Angle : 0.554 7.237 9633 Z= 0.262 Chirality : 0.039 0.118 960 Planarity : 0.005 0.038 1050 Dihedral : 22.926 164.308 1437 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 8.90 % Favored : 88.67 % 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 (0.32), residues: 714 helix: 1.82 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.90 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 186 TYR 0.021 0.002 TYR A 177 PHE 0.022 0.002 PHE C 144 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 7179) covalent geometry : angle 0.55419 / 0.26 ( 9633) hydrogen bonds : bond 0.04108 / 2.76 ( 405) hydrogen bonds : angle 4.13360 / 2.97 ( 1197) Misc. bond : bond 0.00040 / 0.02 ( 6) *********************** 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 143 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.209 Fit side-chains REVERT: A 21 ASP cc_start: 0.8019 (t70) cc_final: 0.7006 (t70) REVERT: A 174 LYS cc_start: 0.8394 (mtmm) cc_final: 0.8152 (mtmt) REVERT: A 183 LYS cc_start: 0.7673 (pttt) cc_final: 0.7440 (pptt) REVERT: B 106 TYR cc_start: 0.8413 (m-80) cc_final: 0.8206 (m-80) REVERT: B 183 LYS cc_start: 0.7684 (pttt) cc_final: 0.7390 (pptt) REVERT: C 81 TYR cc_start: 0.8667 (m-80) cc_final: 0.8385 (m-80) REVERT: C 106 TYR cc_start: 0.8387 (m-80) cc_final: 0.8104 (m-80) REVERT: C 171 ARG cc_start: 0.8050 (ttp80) cc_final: 0.6836 (ttm-80) REVERT: C 183 LYS cc_start: 0.7473 (pttt) cc_final: 0.7170 (pptt) REVERT: C 229 ASP cc_start: 0.8355 (m-30) cc_final: 0.7954 (m-30) outliers start: 15 outliers final: 6 residues processed: 136 average time/residue: 0.4256 time to fit residues: 61.7907 Evaluate side-chains 125 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 43 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 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 = 0.3863 r_free = 0.3863 target = 0.160595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129970 restraints weight = 7063.237| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.43 r_work: 0.3287 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7185 Z= 0.121 Angle : 0.533 7.799 9633 Z= 0.251 Chirality : 0.038 0.119 960 Planarity : 0.004 0.039 1050 Dihedral : 20.810 153.698 1437 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.94 % Allowed : 9.87 % Favored : 88.19 % 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: 1.91 (0.32), residues: 714 helix: 1.97 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.89 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.026 0.001 TYR C 177 PHE 0.022 0.001 PHE C 144 TRP 0.010 0.001 TRP C 42 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7179) covalent geometry : angle 0.53342 / 0.25 ( 9633) hydrogen bonds : bond 0.03753 / 2.52 ( 405) hydrogen bonds : angle 3.96590 / 2.85 ( 1197) Misc. bond : bond 0.00028 / 0.02 ( 6) *********************** 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 142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.166 Fit side-chains REVERT: A 21 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.6961 (t70) REVERT: A 174 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8109 (mtmt) REVERT: A 183 LYS cc_start: 0.7617 (pttt) cc_final: 0.7389 (pptt) REVERT: B 106 TYR cc_start: 0.8394 (m-80) cc_final: 0.8062 (m-80) REVERT: B 171 ARG cc_start: 0.7951 (ttp80) cc_final: 0.6833 (ttm-80) REVERT: B 183 LYS cc_start: 0.7654 (pttt) cc_final: 0.7321 (pptt) REVERT: C 106 TYR cc_start: 0.8397 (m-80) cc_final: 0.8064 (m-80) REVERT: C 171 ARG cc_start: 0.7948 (ttp80) cc_final: 0.6689 (ttm-80) REVERT: C 183 LYS cc_start: 0.7502 (pttt) cc_final: 0.7107 (pptt) REVERT: C 229 ASP cc_start: 0.8215 (m-30) cc_final: 0.7812 (m-30) outliers start: 12 outliers final: 3 residues processed: 135 average time/residue: 0.4145 time to fit residues: 59.8800 Evaluate side-chains 124 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 125 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126047 restraints weight = 7034.188| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.39 r_work: 0.3244 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7185 Z= 0.133 Angle : 0.542 9.203 9633 Z= 0.255 Chirality : 0.039 0.123 960 Planarity : 0.005 0.040 1050 Dihedral : 19.822 154.880 1437 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.59 % Allowed : 10.36 % Favored : 87.06 % 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: 1.95 (0.32), residues: 714 helix: 2.05 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.01 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.035 0.002 TYR A 177 PHE 0.026 0.002 PHE A 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 7179) covalent geometry : angle 0.54239 / 0.26 ( 9633) hydrogen bonds : bond 0.03770 / 2.53 ( 405) hydrogen bonds : angle 3.94826 / 2.83 ( 1197) Misc. bond : bond 0.00032 / 0.02 ( 6) *********************** 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 145 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.231 Fit side-chains REVERT: A 21 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7045 (t70) REVERT: A 174 LYS cc_start: 0.8402 (mtmm) cc_final: 0.8119 (mtmt) REVERT: A 183 LYS cc_start: 0.7595 (pttt) cc_final: 0.7392 (pptt) REVERT: B 106 TYR cc_start: 0.8450 (m-80) cc_final: 0.8246 (m-80) REVERT: B 183 LYS cc_start: 0.7623 (pttt) cc_final: 0.7373 (pptt) REVERT: B 229 ASP cc_start: 0.8380 (m-30) cc_final: 0.7878 (m-30) REVERT: C 106 TYR cc_start: 0.8460 (m-80) cc_final: 0.8085 (m-80) REVERT: C 183 LYS cc_start: 0.7523 (pttt) cc_final: 0.7187 (pptt) REVERT: C 229 ASP cc_start: 0.8338 (m-30) cc_final: 0.8006 (m-30) outliers start: 16 outliers final: 6 residues processed: 134 average time/residue: 0.4286 time to fit residues: 61.5041 Evaluate side-chains 128 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.0270 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126378 restraints weight = 7070.639| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.38 r_work: 0.3263 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7185 Z= 0.136 Angle : 0.547 7.676 9633 Z= 0.260 Chirality : 0.039 0.124 960 Planarity : 0.005 0.041 1050 Dihedral : 18.917 156.034 1437 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.59 % Allowed : 11.17 % Favored : 86.25 % 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: 1.95 (0.32), residues: 714 helix: 2.03 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.99 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.032 0.002 TYR A 177 PHE 0.028 0.002 PHE A 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7179) covalent geometry : angle 0.54683 / 0.26 ( 9633) hydrogen bonds : bond 0.03797 / 2.54 ( 405) hydrogen bonds : angle 3.96042 / 2.84 ( 1197) Misc. bond : bond 0.00031 / 0.02 ( 6) *********************** 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 145 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.244 Fit side-chains REVERT: A 21 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.6951 (t70) REVERT: A 174 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8029 (mtmt) REVERT: A 183 LYS cc_start: 0.7598 (pttt) cc_final: 0.7338 (pptt) REVERT: B 106 TYR cc_start: 0.8394 (m-80) cc_final: 0.8147 (m-80) REVERT: B 183 LYS cc_start: 0.7607 (pttt) cc_final: 0.7324 (pptt) REVERT: B 229 ASP cc_start: 0.8375 (m-30) cc_final: 0.7876 (m-30) REVERT: C 21 ASP cc_start: 0.8038 (t0) cc_final: 0.7313 (t70) REVERT: C 106 TYR cc_start: 0.8440 (m-80) cc_final: 0.8098 (m-80) REVERT: C 183 LYS cc_start: 0.7493 (pttt) cc_final: 0.7081 (pptt) REVERT: C 229 ASP cc_start: 0.8228 (m-30) cc_final: 0.7913 (m-30) outliers start: 16 outliers final: 9 residues processed: 138 average time/residue: 0.3994 time to fit residues: 59.2040 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127040 restraints weight = 7049.989| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.40 r_work: 0.3202 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7185 Z= 0.161 Angle : 0.589 9.730 9633 Z= 0.277 Chirality : 0.040 0.124 960 Planarity : 0.005 0.042 1050 Dihedral : 18.544 159.625 1437 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.91 % Allowed : 11.33 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.32), residues: 714 helix: 1.92 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.06 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.031 0.002 TYR C 177 PHE 0.030 0.002 PHE A 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 7179) covalent geometry : angle 0.58867 / 0.28 ( 9633) hydrogen bonds : bond 0.03980 / 2.67 ( 405) hydrogen bonds : angle 4.02944 / 2.88 ( 1197) Misc. bond : bond 0.00037 / 0.02 ( 6) *********************** 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 142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.236 Fit side-chains REVERT: A 21 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.6927 (t70) REVERT: A 174 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7937 (mtmt) REVERT: A 183 LYS cc_start: 0.7569 (pttt) cc_final: 0.7290 (pptt) REVERT: B 106 TYR cc_start: 0.8378 (m-80) cc_final: 0.8112 (m-80) REVERT: B 183 LYS cc_start: 0.7634 (pttt) cc_final: 0.7322 (pptt) REVERT: B 186 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7400 (ttt90) REVERT: C 90 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: C 106 TYR cc_start: 0.8469 (m-80) cc_final: 0.8105 (m-80) REVERT: C 183 LYS cc_start: 0.7524 (pttt) cc_final: 0.7082 (pptt) REVERT: C 229 ASP cc_start: 0.8241 (m-30) cc_final: 0.7966 (m-30) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.4016 time to fit residues: 55.9539 Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128668 restraints weight = 7097.270| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.39 r_work: 0.3320 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7185 Z= 0.126 Angle : 0.542 8.562 9633 Z= 0.261 Chirality : 0.039 0.124 960 Planarity : 0.005 0.042 1050 Dihedral : 17.885 158.106 1437 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.10 % Allowed : 12.62 % Favored : 85.28 % 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: 1.94 (0.32), residues: 714 helix: 2.04 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.06 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.035 0.002 TYR C 177 PHE 0.030 0.001 PHE A 144 TRP 0.012 0.001 TRP A 42 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7179) covalent geometry : angle 0.54152 / 0.26 ( 9633) hydrogen bonds : bond 0.03720 / 2.50 ( 405) hydrogen bonds : angle 3.96853 / 2.84 ( 1197) Misc. bond : bond 0.00025 / 0.01 ( 6) *********************** 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 145 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.222 Fit side-chains REVERT: A 21 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.6954 (t70) REVERT: A 174 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7991 (mtmt) REVERT: A 183 LYS cc_start: 0.7387 (pttt) cc_final: 0.7139 (pptt) REVERT: B 106 TYR cc_start: 0.8394 (m-80) cc_final: 0.8129 (m-80) REVERT: B 183 LYS cc_start: 0.7594 (pttt) cc_final: 0.7290 (pptt) REVERT: B 186 ARG cc_start: 0.7578 (ttt90) cc_final: 0.7315 (ttt90) REVERT: B 229 ASP cc_start: 0.8304 (m-30) cc_final: 0.7804 (m-30) REVERT: C 21 ASP cc_start: 0.7948 (t70) cc_final: 0.7246 (t70) REVERT: C 106 TYR cc_start: 0.8488 (m-80) cc_final: 0.8136 (m-80) REVERT: C 183 LYS cc_start: 0.7482 (pttt) cc_final: 0.7063 (pptt) REVERT: C 229 ASP cc_start: 0.8208 (m-30) cc_final: 0.7927 (m-30) outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.3974 time to fit residues: 58.1126 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS A 185 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129598 restraints weight = 7018.210| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.37 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7185 Z= 0.136 Angle : 0.568 8.437 9633 Z= 0.272 Chirality : 0.039 0.123 960 Planarity : 0.005 0.042 1050 Dihedral : 17.748 159.587 1437 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.75 % Allowed : 11.97 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.32), residues: 714 helix: 1.99 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.06 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 186 TYR 0.033 0.001 TYR B 177 PHE 0.033 0.002 PHE A 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7179) covalent geometry : angle 0.56753 / 0.27 ( 9633) hydrogen bonds : bond 0.03845 / 2.58 ( 405) hydrogen bonds : angle 4.01112 / 2.87 ( 1197) Misc. bond : bond 0.00032 / 0.02 ( 6) *********************** 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 147 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.137 Fit side-chains REVERT: A 21 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.6933 (t70) REVERT: A 174 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7833 (mtmp) REVERT: A 183 LYS cc_start: 0.7399 (pttt) cc_final: 0.7146 (pptt) REVERT: B 106 TYR cc_start: 0.8388 (m-80) cc_final: 0.8111 (m-80) REVERT: B 183 LYS cc_start: 0.7609 (pttt) cc_final: 0.7281 (pptt) REVERT: B 186 ARG cc_start: 0.7536 (ttt90) cc_final: 0.7274 (ttt90) REVERT: B 229 ASP cc_start: 0.8269 (m-30) cc_final: 0.7756 (m-30) REVERT: C 21 ASP cc_start: 0.7970 (t70) cc_final: 0.7237 (t70) REVERT: C 106 TYR cc_start: 0.8492 (m-80) cc_final: 0.8161 (m-80) REVERT: C 171 ARG cc_start: 0.7723 (mtm110) cc_final: 0.6784 (ttm-80) REVERT: C 183 LYS cc_start: 0.7458 (pttt) cc_final: 0.7064 (pptt) REVERT: C 229 ASP cc_start: 0.8184 (m-30) cc_final: 0.7823 (m-30) outliers start: 17 outliers final: 10 residues processed: 137 average time/residue: 0.3650 time to fit residues: 53.7843 Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129813 restraints weight = 6997.168| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.38 r_work: 0.3318 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7185 Z= 0.133 Angle : 0.576 11.372 9633 Z= 0.275 Chirality : 0.039 0.123 960 Planarity : 0.005 0.042 1050 Dihedral : 17.572 160.528 1437 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.59 % Allowed : 12.78 % Favored : 84.63 % 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: 1.91 (0.32), residues: 714 helix: 2.02 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.07 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 171 TYR 0.034 0.001 TYR C 177 PHE 0.034 0.002 PHE A 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 7179) covalent geometry : angle 0.57627 / 0.27 ( 9633) hydrogen bonds : bond 0.03843 / 2.57 ( 405) hydrogen bonds : angle 4.02847 / 2.88 ( 1197) Misc. bond : bond 0.00033 / 0.02 ( 6) ********************** 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 143 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.227 Fit side-chains REVERT: A 21 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.6989 (t70) REVERT: A 174 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7951 (mtmp) REVERT: A 183 LYS cc_start: 0.7361 (pttt) cc_final: 0.7082 (pptt) REVERT: B 106 TYR cc_start: 0.8410 (m-80) cc_final: 0.8152 (m-80) REVERT: B 183 LYS cc_start: 0.7613 (pttt) cc_final: 0.7284 (pptt) REVERT: B 186 ARG cc_start: 0.7454 (ttt90) cc_final: 0.7178 (ttt90) REVERT: B 229 ASP cc_start: 0.8247 (m-30) cc_final: 0.7739 (m-30) REVERT: C 21 ASP cc_start: 0.7968 (t70) cc_final: 0.7248 (t70) REVERT: C 106 TYR cc_start: 0.8505 (m-80) cc_final: 0.8162 (m-80) REVERT: C 171 ARG cc_start: 0.7732 (mtm110) cc_final: 0.6783 (ttm-80) REVERT: C 183 LYS cc_start: 0.7442 (pttt) cc_final: 0.7048 (pptt) REVERT: C 229 ASP cc_start: 0.8164 (m-30) cc_final: 0.7828 (m-30) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.3994 time to fit residues: 56.6981 Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129466 restraints weight = 7019.326| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.37 r_work: 0.3295 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7185 Z= 0.143 Angle : 0.590 10.884 9633 Z= 0.281 Chirality : 0.040 0.128 960 Planarity : 0.005 0.042 1050 Dihedral : 17.560 162.173 1437 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.91 % Allowed : 13.11 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.31), residues: 714 helix: 1.95 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.09 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 171 TYR 0.033 0.001 TYR B 177 PHE 0.034 0.002 PHE B 144 TRP 0.010 0.001 TRP A 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 7179) covalent geometry : angle 0.59022 / 0.28 ( 9633) hydrogen bonds : bond 0.03927 / 2.63 ( 405) hydrogen bonds : angle 4.06804 / 2.90 ( 1197) Misc. bond : bond 0.00035 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.38 seconds wall clock time: 37 minutes 21.59 seconds (2241.59 seconds total)