Starting phenix.real_space_refine on Wed Feb 12 07:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_40062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_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/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_40062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_40062.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_40062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi8_40062/02_2025/8gi8_40062.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B Time building chain proxies: 3.92, per 1000 atoms: 0.56 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: 2.17 Conformation dependent library (CDL) restraints added in 828.7 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: 0.55 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: 1.87 Time building geometry restraints manager: 2.45 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: 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: 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.920 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.850 Find NCS groups from input model: 0.130 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- 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= 0.621 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 to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.710 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: 0.9524 time to fit residues: 126.2852 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 : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.0170 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 overall best weight: 0.1994 ------------------------------------------------------------------------------- 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 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124732 restraints weight = 7111.246| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.39 r_work: 0.3226 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.186 7179 Z= 0.605 Angle : 1.452 40.076 9633 Z= 0.711 Chirality : 0.062 0.539 960 Planarity : 0.017 0.180 1050 Dihedral : 30.657 173.577 2091 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.52 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 7.93 % Favored : 90.29 % 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: -0.54 (0.30), residues: 714 helix: 0.09 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.39 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.009 TRP B 138 HIS 0.020 0.002 HIS C 125 PHE 0.200 0.007 PHE C 227 TYR 0.202 0.011 TYR B 177 ARG 0.062 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 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.680 Fit side-chains REVERT: A 21 ASP cc_start: 0.7929 (t70) cc_final: 0.7013 (t70) REVERT: A 106 TYR cc_start: 0.8476 (m-80) cc_final: 0.8067 (m-80) REVERT: A 108 PHE cc_start: 0.8217 (m-80) cc_final: 0.7800 (m-80) REVERT: A 174 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8219 (mtmt) REVERT: B 21 ASP cc_start: 0.7869 (t70) cc_final: 0.7270 (t70) REVERT: B 106 TYR cc_start: 0.8355 (m-80) cc_final: 0.8038 (m-80) REVERT: B 108 PHE cc_start: 0.8249 (m-80) cc_final: 0.7877 (m-80) REVERT: C 21 ASP cc_start: 0.7942 (t70) cc_final: 0.7205 (t70) REVERT: C 106 TYR cc_start: 0.8357 (m-80) cc_final: 0.8067 (m-80) REVERT: C 177 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.8141 (t80) REVERT: C 227 PHE cc_start: 0.7541 (m-80) cc_final: 0.7203 (m-80) REVERT: C 240 MET cc_start: 0.7833 (mmp) cc_final: 0.7619 (mmm) REVERT: C 246 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7556 (mt-10) outliers start: 11 outliers final: 1 residues processed: 131 average time/residue: 0.8566 time to fit residues: 120.8069 Evaluate side-chains 110 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 72 random chunks: chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 185 GLN B 218 GLN C 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127347 restraints weight = 7073.979| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.43 r_work: 0.3215 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1949 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= 0.249 Angle : 0.604 6.700 9633 Z= 0.288 Chirality : 0.041 0.164 960 Planarity : 0.005 0.048 1050 Dihedral : 27.916 178.870 2091 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.24 % Favored : 97.62 % Rotamer: Outliers : 1.46 % Allowed : 10.52 % Favored : 88.03 % 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: 1.20 (0.32), residues: 714 helix: 1.40 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -0.90 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.004 0.001 HIS B 172 PHE 0.016 0.002 PHE B 134 TYR 0.033 0.002 TYR B 177 ARG 0.004 0.001 ARG B 244 *********************** 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 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.701 Fit side-chains REVERT: A 21 ASP cc_start: 0.7869 (t70) cc_final: 0.6826 (t70) REVERT: A 174 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8083 (mtmt) REVERT: A 183 LYS cc_start: 0.7641 (pttt) cc_final: 0.7420 (pptt) REVERT: B 106 TYR cc_start: 0.8416 (m-80) cc_final: 0.8153 (m-80) REVERT: B 170 MET cc_start: 0.8216 (mtt) cc_final: 0.7836 (mtt) REVERT: B 183 LYS cc_start: 0.7661 (pttt) cc_final: 0.7349 (pptt) REVERT: B 186 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7207 (ttt90) REVERT: C 21 ASP cc_start: 0.8104 (t70) cc_final: 0.7823 (t0) REVERT: C 106 TYR cc_start: 0.8426 (m-80) cc_final: 0.8059 (m-80) REVERT: C 229 ASP cc_start: 0.8361 (m-30) cc_final: 0.7810 (m-30) outliers start: 9 outliers final: 3 residues processed: 124 average time/residue: 0.9798 time to fit residues: 130.0206 Evaluate side-chains 108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain C residue 105 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126013 restraints weight = 7143.509| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.44 r_work: 0.3199 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2203 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= 0.243 Angle : 0.588 6.005 9633 Z= 0.278 Chirality : 0.041 0.165 960 Planarity : 0.005 0.041 1050 Dihedral : 25.989 178.879 2091 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.80 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 11.33 % Favored : 86.73 % 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: 1.55 (0.32), residues: 714 helix: 1.65 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.004 0.001 HIS B 172 PHE 0.026 0.002 PHE C 144 TYR 0.024 0.002 TYR B 177 ARG 0.004 0.001 ARG C 171 *********************** 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 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.672 Fit side-chains REVERT: A 21 ASP cc_start: 0.7911 (t70) cc_final: 0.6886 (t70) REVERT: A 174 LYS cc_start: 0.8265 (mtmm) cc_final: 0.8038 (mtmt) REVERT: A 183 LYS cc_start: 0.7658 (pttt) cc_final: 0.7403 (pptt) REVERT: B 106 TYR cc_start: 0.8489 (m-80) cc_final: 0.8270 (m-80) REVERT: B 170 MET cc_start: 0.8226 (mtt) cc_final: 0.7832 (mtt) REVERT: B 183 LYS cc_start: 0.7629 (pttt) cc_final: 0.7302 (pptt) REVERT: C 106 TYR cc_start: 0.8455 (m-80) cc_final: 0.8090 (m-80) REVERT: C 174 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7977 (mtpp) REVERT: C 183 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7599 (pptt) REVERT: C 229 ASP cc_start: 0.8395 (m-30) cc_final: 0.7903 (m-30) outliers start: 12 outliers final: 5 residues processed: 127 average time/residue: 0.9461 time to fit residues: 128.2970 Evaluate side-chains 119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3841 r_free = 0.3841 target = 0.158914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128152 restraints weight = 7017.278| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.41 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7179 Z= 0.217 Angle : 0.580 8.633 9633 Z= 0.274 Chirality : 0.040 0.161 960 Planarity : 0.005 0.041 1050 Dihedral : 24.342 165.392 2091 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.10 % Allowed : 12.46 % Favored : 85.44 % 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: 1.73 (0.32), residues: 714 helix: 1.85 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -0.95 (0.53), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 42 HIS 0.003 0.001 HIS B 172 PHE 0.026 0.002 PHE C 144 TYR 0.011 0.001 TYR A 81 ARG 0.003 0.001 ARG C 186 *********************** 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.690 Fit side-chains REVERT: A 21 ASP cc_start: 0.7893 (t70) cc_final: 0.6907 (t70) REVERT: A 174 LYS cc_start: 0.8281 (mtmm) cc_final: 0.8027 (mtmt) REVERT: A 183 LYS cc_start: 0.7648 (pttt) cc_final: 0.7415 (pptt) REVERT: B 170 MET cc_start: 0.8261 (mtt) cc_final: 0.7884 (mtt) REVERT: B 183 LYS cc_start: 0.7620 (pttt) cc_final: 0.7297 (pptt) REVERT: C 21 ASP cc_start: 0.8027 (t0) cc_final: 0.7222 (t70) REVERT: C 106 TYR cc_start: 0.8442 (m-80) cc_final: 0.8053 (m-80) REVERT: C 183 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7552 (pptt) REVERT: C 229 ASP cc_start: 0.8365 (m-30) cc_final: 0.7909 (m-30) outliers start: 13 outliers final: 4 residues processed: 131 average time/residue: 0.9323 time to fit residues: 130.6187 Evaluate side-chains 126 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 125 HIS ** 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 = 0.3825 r_free = 0.3825 target = 0.157613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126652 restraints weight = 7075.409| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.41 r_work: 0.3218 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7179 Z= 0.242 Angle : 0.610 9.858 9633 Z= 0.284 Chirality : 0.040 0.161 960 Planarity : 0.005 0.043 1050 Dihedral : 23.576 170.186 2091 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.10 % Allowed : 13.11 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.32), residues: 714 helix: 1.87 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.05 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.028 0.002 PHE A 144 TYR 0.031 0.002 TYR A 177 ARG 0.004 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 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.599 Fit side-chains REVERT: A 21 ASP cc_start: 0.7834 (t70) cc_final: 0.6856 (t70) REVERT: A 174 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7966 (mtmt) REVERT: A 183 LYS cc_start: 0.7651 (pttt) cc_final: 0.7393 (pptt) REVERT: B 170 MET cc_start: 0.8212 (mtt) cc_final: 0.7893 (mtt) REVERT: B 183 LYS cc_start: 0.7635 (pttt) cc_final: 0.7283 (pptt) REVERT: C 90 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: C 106 TYR cc_start: 0.8442 (m-80) cc_final: 0.8056 (m-80) REVERT: C 183 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7531 (pptt) REVERT: C 229 ASP cc_start: 0.8422 (m-30) cc_final: 0.7958 (m-30) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.9680 time to fit residues: 127.0939 Evaluate side-chains 122 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 125 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.157163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127492 restraints weight = 7124.275| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.35 r_work: 0.3192 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7179 Z= 0.250 Angle : 0.620 9.535 9633 Z= 0.289 Chirality : 0.041 0.161 960 Planarity : 0.005 0.043 1050 Dihedral : 22.919 173.605 2091 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.10 % Allowed : 13.75 % Favored : 84.14 % 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: 1.66 (0.32), residues: 714 helix: 1.85 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.030 0.002 PHE C 144 TYR 0.033 0.002 TYR C 177 ARG 0.005 0.001 ARG A 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 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.714 Fit side-chains REVERT: A 21 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.6931 (t70) REVERT: A 174 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8093 (mtmt) REVERT: A 183 LYS cc_start: 0.7599 (pttt) cc_final: 0.7279 (pptt) REVERT: A 240 MET cc_start: 0.7737 (mmp) cc_final: 0.7483 (mmm) REVERT: B 170 MET cc_start: 0.8333 (mtt) cc_final: 0.8019 (mtt) REVERT: B 183 LYS cc_start: 0.7682 (pttt) cc_final: 0.7337 (pptt) REVERT: C 51 MET cc_start: 0.5257 (ttm) cc_final: 0.4566 (ttp) REVERT: C 81 TYR cc_start: 0.8549 (m-80) cc_final: 0.8248 (m-80) REVERT: C 106 TYR cc_start: 0.8490 (m-80) cc_final: 0.8156 (m-80) REVERT: C 183 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7538 (pptt) REVERT: C 229 ASP cc_start: 0.8442 (m-30) cc_final: 0.8000 (m-30) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 0.9298 time to fit residues: 125.5286 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 201 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 183 LYS 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 39 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3874 r_free = 0.3874 target = 0.161685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131640 restraints weight = 7043.248| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.40 r_work: 0.3213 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7179 Z= 0.231 Angle : 0.609 8.840 9633 Z= 0.286 Chirality : 0.041 0.158 960 Planarity : 0.005 0.044 1050 Dihedral : 22.286 178.296 2091 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.10 % Allowed : 14.40 % Favored : 83.50 % 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: 1.75 (0.32), residues: 714 helix: 1.92 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.13 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.031 0.002 PHE C 144 TYR 0.034 0.002 TYR C 177 ARG 0.005 0.001 ARG C 171 *********************** 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.6933 (t70) REVERT: A 174 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8054 (mtmt) REVERT: A 183 LYS cc_start: 0.7405 (pttt) cc_final: 0.7085 (pptt) REVERT: B 170 MET cc_start: 0.8318 (mtt) cc_final: 0.7961 (mtt) REVERT: B 171 ARG cc_start: 0.7612 (mtm110) cc_final: 0.6793 (ttm-80) REVERT: B 183 LYS cc_start: 0.7641 (pttt) cc_final: 0.7287 (pptt) REVERT: C 21 ASP cc_start: 0.7893 (t70) cc_final: 0.7459 (t70) REVERT: C 51 MET cc_start: 0.4993 (ttm) cc_final: 0.4381 (ttp) REVERT: C 81 TYR cc_start: 0.8673 (m-80) cc_final: 0.8376 (m-80) REVERT: C 106 TYR cc_start: 0.8485 (m-80) cc_final: 0.8126 (m-80) REVERT: C 183 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7467 (pptt) REVERT: C 229 ASP cc_start: 0.8416 (m-30) cc_final: 0.7941 (m-30) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.9481 time to fit residues: 132.8497 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 201 MET 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 137 LEU Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133790 restraints weight = 7101.643| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.40 r_work: 0.3230 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7179 Z= 0.203 Angle : 0.602 10.260 9633 Z= 0.283 Chirality : 0.040 0.154 960 Planarity : 0.005 0.043 1050 Dihedral : 21.436 177.199 2091 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.78 % Allowed : 15.05 % Favored : 83.17 % 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: 1.79 (0.32), residues: 714 helix: 1.94 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.10 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 42 HIS 0.002 0.001 HIS B 172 PHE 0.031 0.002 PHE A 144 TYR 0.034 0.001 TYR B 177 ARG 0.006 0.001 ARG C 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 141 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.660 Fit side-chains REVERT: A 21 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.6816 (t70) REVERT: A 174 LYS cc_start: 0.8342 (mtmm) cc_final: 0.8035 (mtmt) REVERT: A 183 LYS cc_start: 0.7384 (pttt) cc_final: 0.7063 (pptt) REVERT: B 106 TYR cc_start: 0.8331 (m-80) cc_final: 0.7984 (m-80) REVERT: B 170 MET cc_start: 0.8297 (mtt) cc_final: 0.7956 (mtt) REVERT: B 171 ARG cc_start: 0.7601 (mtm110) cc_final: 0.6829 (ttm-80) REVERT: B 183 LYS cc_start: 0.7643 (pttt) cc_final: 0.7298 (pptt) REVERT: C 21 ASP cc_start: 0.7918 (t70) cc_final: 0.7433 (t70) REVERT: C 51 MET cc_start: 0.4988 (ttm) cc_final: 0.4426 (ttp) REVERT: C 81 TYR cc_start: 0.8445 (m-80) cc_final: 0.8098 (m-80) REVERT: C 106 TYR cc_start: 0.8460 (m-80) cc_final: 0.8049 (m-80) REVERT: C 183 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7456 (pptt) REVERT: C 229 ASP cc_start: 0.8304 (m-30) cc_final: 0.7800 (m-30) outliers start: 11 outliers final: 6 residues processed: 132 average time/residue: 0.9389 time to fit residues: 132.8371 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133347 restraints weight = 7133.420| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.42 r_work: 0.3217 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7179 Z= 0.207 Angle : 0.609 9.913 9633 Z= 0.289 Chirality : 0.041 0.154 960 Planarity : 0.005 0.043 1050 Dihedral : 20.709 174.592 2091 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.46 % Allowed : 16.02 % Favored : 82.52 % 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: 1.82 (0.32), residues: 714 helix: 1.96 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.08 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.034 0.002 PHE A 144 TYR 0.034 0.001 TYR C 177 ARG 0.007 0.001 ARG A 171 ********************** 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.683 Fit side-chains REVERT: A 21 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.6762 (t70) REVERT: A 174 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7996 (mtmt) REVERT: A 183 LYS cc_start: 0.7356 (pttt) cc_final: 0.7033 (pptt) REVERT: B 106 TYR cc_start: 0.8408 (m-80) cc_final: 0.7660 (m-80) REVERT: B 170 MET cc_start: 0.8277 (mtt) cc_final: 0.7932 (mtt) REVERT: B 171 ARG cc_start: 0.7589 (mtm110) cc_final: 0.6814 (ttm-80) REVERT: B 183 LYS cc_start: 0.7608 (pttt) cc_final: 0.7251 (pptt) REVERT: B 229 ASP cc_start: 0.8173 (m-30) cc_final: 0.7722 (m-30) REVERT: C 21 ASP cc_start: 0.7939 (t70) cc_final: 0.7409 (t70) REVERT: C 51 MET cc_start: 0.4964 (ttm) cc_final: 0.4407 (ttp) REVERT: C 81 TYR cc_start: 0.8579 (m-80) cc_final: 0.8252 (m-80) REVERT: C 106 TYR cc_start: 0.8452 (m-80) cc_final: 0.8011 (m-80) REVERT: C 183 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7503 (pptt) REVERT: C 229 ASP cc_start: 0.8327 (m-30) cc_final: 0.7822 (m-30) outliers start: 9 outliers final: 6 residues processed: 131 average time/residue: 0.9415 time to fit residues: 132.0428 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 183 LYS 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 4 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** 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 = 0.3869 r_free = 0.3869 target = 0.161187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130565 restraints weight = 7049.111| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.41 r_work: 0.3230 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2964 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= 0.222 Angle : 0.625 9.779 9633 Z= 0.296 Chirality : 0.041 0.155 960 Planarity : 0.005 0.043 1050 Dihedral : 20.284 167.616 2091 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.94 % Allowed : 16.34 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.32), residues: 714 helix: 1.90 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.09 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.035 0.002 PHE A 144 TYR 0.034 0.001 TYR B 177 ARG 0.006 0.001 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4356.72 seconds wall clock time: 77 minutes 58.47 seconds (4678.47 seconds total)