Starting phenix.real_space_refine on Wed Mar 12 07:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi8_40062/03_2025/8gi8_40062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi8_40062/03_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_40062/03_2025/8gi8_40062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi8_40062/03_2025/8gi8_40062.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi8_40062/03_2025/8gi8_40062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi8_40062/03_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-5624/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: 5.15, per 1000 atoms: 0.74 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 822.5 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... 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: 0.61 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: 1.96 Time building geometry restraints manager: 2.51 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: 1.010 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.040 Find NCS groups from input model: 0.140 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:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- 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 : 0.652 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: 0.9114 time to fit residues: 120.9632 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 : 0.703 ------------------------------------------------------------------------------- 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 : 0.696 Fit side-chains REVERT: A 21 ASP cc_start: 0.7929 (t70) cc_final: 0.7014 (t70) REVERT: A 106 TYR cc_start: 0.8476 (m-80) cc_final: 0.8068 (m-80) REVERT: A 108 PHE cc_start: 0.8218 (m-80) cc_final: 0.7801 (m-80) REVERT: A 174 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8219 (mtmt) REVERT: B 21 ASP cc_start: 0.7868 (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: 0.7878 (m-80) REVERT: C 21 ASP cc_start: 0.7942 (t70) cc_final: 0.7206 (t70) REVERT: C 106 TYR cc_start: 0.8356 (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: 0.7202 (m-80) REVERT: C 240 MET cc_start: 0.7834 (mmp) cc_final: 0.7620 (mmm) REVERT: C 246 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7557 (mt-10) outliers start: 11 outliers final: 1 residues processed: 131 average time/residue: 0.8180 time to fit residues: 115.7440 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 : 0.597 ------------------------------------------------------------------------------- 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: 0.3216 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: 0.7836 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 : 0.623 Fit side-chains REVERT: A 21 ASP cc_start: 0.7869 (t70) cc_final: 0.6831 (t70) REVERT: A 174 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8083 (mtmt) REVERT: A 183 LYS cc_start: 0.7643 (pttt) cc_final: 0.7424 (pptt) REVERT: B 106 TYR cc_start: 0.8419 (m-80) cc_final: 0.8158 (m-80) REVERT: B 170 MET cc_start: 0.8211 (mtt) cc_final: 0.7831 (mtt) REVERT: B 183 LYS cc_start: 0.7665 (pttt) cc_final: 0.7353 (pptt) REVERT: B 186 ARG cc_start: 0.7432 (ttt90) cc_final: 0.7211 (ttt90) REVERT: C 21 ASP cc_start: 0.8104 (t70) cc_final: 0.7823 (t0) REVERT: C 106 TYR cc_start: 0.8429 (m-80) cc_final: 0.8063 (m-80) REVERT: C 229 ASP cc_start: 0.8362 (m-30) cc_final: 0.7813 (m-30) outliers start: 9 outliers final: 3 residues processed: 124 average time/residue: 0.9131 time to fit residues: 121.1277 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 : 0.626 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** 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 = 0.3827 r_free = 0.3827 target = 0.157348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126237 restraints weight = 7129.822| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.44 r_work: 0.3203 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7179 Z= 0.238 Angle : 0.585 5.897 9633 Z= 0.276 Chirality : 0.041 0.165 960 Planarity : 0.005 0.041 1050 Dihedral : 25.773 178.419 2091 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.80 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 11.65 % Favored : 86.57 % 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: 1.57 (0.32), residues: 714 helix: 1.68 (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 C 250 PHE 0.028 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 140 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.604 Fit side-chains REVERT: A 21 ASP cc_start: 0.7924 (t70) cc_final: 0.6913 (t70) REVERT: A 174 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8095 (mtmt) REVERT: A 183 LYS cc_start: 0.7661 (pttt) cc_final: 0.7409 (pptt) REVERT: B 106 TYR cc_start: 0.8500 (m-80) cc_final: 0.8284 (m-80) REVERT: B 170 MET cc_start: 0.8219 (mtt) cc_final: 0.7827 (mtt) REVERT: B 183 LYS cc_start: 0.7614 (pttt) cc_final: 0.7290 (pptt) REVERT: B 186 ARG cc_start: 0.7573 (ttt90) cc_final: 0.7357 (ttt90) REVERT: C 81 TYR cc_start: 0.8493 (m-80) cc_final: 0.8260 (m-80) REVERT: C 106 TYR cc_start: 0.8457 (m-80) cc_final: 0.8124 (m-80) REVERT: C 150 TYR cc_start: 0.8350 (m-80) cc_final: 0.8111 (m-80) REVERT: C 183 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7554 (pmtt) REVERT: C 229 ASP cc_start: 0.8410 (m-30) cc_final: 0.7915 (m-30) outliers start: 11 outliers final: 4 residues processed: 134 average time/residue: 0.9161 time to fit residues: 131.1923 Evaluate side-chains 125 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 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 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 185 GLN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.158654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127949 restraints weight = 7029.722| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.42 r_work: 0.3196 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7179 Z= 0.236 Angle : 0.599 8.658 9633 Z= 0.281 Chirality : 0.040 0.164 960 Planarity : 0.005 0.042 1050 Dihedral : 24.617 164.766 2091 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.10 % Allowed : 12.30 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.32), residues: 714 helix: 1.80 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.00 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS B 172 PHE 0.027 0.002 PHE C 144 TYR 0.011 0.001 TYR A 177 ARG 0.004 0.001 ARG C 171 *********************** 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 140 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.623 Fit side-chains REVERT: A 21 ASP cc_start: 0.7906 (t70) cc_final: 0.6893 (t70) REVERT: A 174 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8032 (mtmt) REVERT: A 183 LYS cc_start: 0.7670 (pttt) cc_final: 0.7420 (pptt) REVERT: B 170 MET cc_start: 0.8266 (mtt) cc_final: 0.7880 (mtt) REVERT: B 183 LYS cc_start: 0.7617 (pttt) cc_final: 0.7291 (pptt) REVERT: C 81 TYR cc_start: 0.8486 (m-80) cc_final: 0.8193 (m-80) REVERT: C 106 TYR cc_start: 0.8448 (m-80) cc_final: 0.8071 (m-80) REVERT: C 183 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7588 (pptt) REVERT: C 229 ASP cc_start: 0.8404 (m-30) cc_final: 0.7932 (m-30) outliers start: 13 outliers final: 6 residues processed: 133 average time/residue: 0.9671 time to fit residues: 137.6263 Evaluate side-chains 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 69 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 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 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 = 0.3826 r_free = 0.3826 target = 0.157712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126818 restraints weight = 7071.631| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.41 r_work: 0.3181 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7179 Z= 0.234 Angle : 0.601 8.799 9633 Z= 0.282 Chirality : 0.040 0.161 960 Planarity : 0.005 0.043 1050 Dihedral : 23.627 169.427 2091 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 1.71 (0.32), residues: 714 helix: 1.87 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.06 (0.52), 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 0.029 0.002 PHE A 144 TYR 0.033 0.002 TYR A 177 ARG 0.005 0.001 ARG C 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 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.660 Fit side-chains REVERT: A 21 ASP cc_start: 0.7858 (t70) cc_final: 0.6871 (t70) REVERT: A 174 LYS cc_start: 0.8290 (mtmm) cc_final: 0.8017 (mtmt) REVERT: A 183 LYS cc_start: 0.7666 (pttt) cc_final: 0.7407 (pptt) REVERT: B 106 TYR cc_start: 0.8443 (m-80) cc_final: 0.8189 (m-80) REVERT: B 170 MET cc_start: 0.8248 (mtt) cc_final: 0.7882 (mtt) REVERT: B 183 LYS cc_start: 0.7622 (pttt) cc_final: 0.7278 (pptt) REVERT: C 21 ASP cc_start: 0.7990 (t0) cc_final: 0.7276 (t70) REVERT: C 81 TYR cc_start: 0.8491 (m-80) cc_final: 0.8218 (m-80) REVERT: C 106 TYR cc_start: 0.8487 (m-80) cc_final: 0.8121 (m-80) REVERT: C 183 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7532 (pptt) REVERT: C 229 ASP cc_start: 0.8412 (m-30) cc_final: 0.7977 (m-30) outliers start: 13 outliers final: 9 residues processed: 129 average time/residue: 0.9067 time to fit residues: 125.4025 Evaluate side-chains 126 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128063 restraints weight = 7135.560| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.37 r_work: 0.3181 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7179 Z= 0.263 Angle : 0.634 9.694 9633 Z= 0.295 Chirality : 0.041 0.163 960 Planarity : 0.005 0.044 1050 Dihedral : 22.947 172.964 2091 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 13.75 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.32), residues: 714 helix: 1.78 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.14 (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 0.035 0.002 TYR C 177 ARG 0.005 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.613 Fit side-chains REVERT: A 21 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.6948 (t70) REVERT: A 174 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8034 (mtmt) REVERT: A 183 LYS cc_start: 0.7603 (pttt) cc_final: 0.7303 (pptt) REVERT: B 106 TYR cc_start: 0.8465 (m-80) cc_final: 0.8208 (m-80) REVERT: B 170 MET cc_start: 0.8320 (mtt) cc_final: 0.7989 (mtt) REVERT: B 183 LYS cc_start: 0.7662 (pttt) cc_final: 0.7316 (pptt) REVERT: C 21 ASP cc_start: 0.7975 (t0) cc_final: 0.7258 (t70) REVERT: C 81 TYR cc_start: 0.8573 (m-80) cc_final: 0.8282 (m-80) REVERT: C 106 TYR cc_start: 0.8503 (m-80) cc_final: 0.8140 (m-80) REVERT: C 183 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7552 (pptt) REVERT: C 229 ASP cc_start: 0.8438 (m-30) cc_final: 0.7990 (m-30) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.9008 time to fit residues: 120.5647 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 : 0.605 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain C residue 183 LYS 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: 6.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130747 restraints weight = 7075.315| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.40 r_work: 0.3199 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7179 Z= 0.255 Angle : 0.624 8.963 9633 Z= 0.292 Chirality : 0.041 0.161 960 Planarity : 0.005 0.044 1050 Dihedral : 22.350 176.816 2091 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.43 % Allowed : 13.92 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.32), residues: 714 helix: 1.82 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.15 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 42 HIS 0.003 0.001 HIS B 172 PHE 0.031 0.002 PHE C 144 TYR 0.033 0.002 TYR C 177 ARG 0.005 0.001 ARG A 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 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.698 Fit side-chains REVERT: A 21 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.6984 (t70) REVERT: A 174 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7974 (mtmt) REVERT: A 183 LYS cc_start: 0.7402 (pttt) cc_final: 0.7079 (pptt) REVERT: B 106 TYR cc_start: 0.8494 (m-80) cc_final: 0.8235 (m-80) REVERT: B 170 MET cc_start: 0.8321 (mtt) cc_final: 0.8013 (mtt) REVERT: B 171 ARG cc_start: 0.7639 (mtm110) cc_final: 0.6809 (ttm-80) REVERT: B 183 LYS cc_start: 0.7669 (pttt) cc_final: 0.7312 (pptt) REVERT: B 229 ASP cc_start: 0.8348 (m-30) cc_final: 0.7911 (m-30) REVERT: C 21 ASP cc_start: 0.7981 (t0) cc_final: 0.7245 (t70) REVERT: C 51 MET cc_start: 0.4916 (ttm) cc_final: 0.4196 (mtm) REVERT: C 81 TYR cc_start: 0.8687 (m-80) cc_final: 0.8333 (m-80) REVERT: C 106 TYR cc_start: 0.8487 (m-80) cc_final: 0.8028 (m-80) REVERT: C 150 TYR cc_start: 0.8109 (m-80) cc_final: 0.7885 (m-80) REVERT: C 183 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7514 (pptt) REVERT: C 229 ASP cc_start: 0.8353 (m-30) cc_final: 0.7831 (m-30) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 0.8849 time to fit residues: 119.5158 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 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 185 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131261 restraints weight = 7146.403| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.41 r_work: 0.3188 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7179 Z= 0.246 Angle : 0.631 10.557 9633 Z= 0.295 Chirality : 0.041 0.159 960 Planarity : 0.005 0.044 1050 Dihedral : 21.736 179.535 2091 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 14.40 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.32), residues: 714 helix: 1.80 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.16 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.033 0.002 PHE C 144 TYR 0.035 0.002 TYR B 177 ARG 0.006 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.679 Fit side-chains REVERT: A 21 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.6924 (t70) REVERT: A 174 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7985 (mtmt) REVERT: A 183 LYS cc_start: 0.7379 (pttt) cc_final: 0.7044 (pptt) REVERT: B 106 TYR cc_start: 0.8495 (m-80) cc_final: 0.8230 (m-80) REVERT: B 170 MET cc_start: 0.8335 (mtt) cc_final: 0.8012 (mtt) REVERT: B 183 LYS cc_start: 0.7666 (pttt) cc_final: 0.7307 (pptt) REVERT: B 229 ASP cc_start: 0.8378 (m-30) cc_final: 0.7943 (m-30) REVERT: C 21 ASP cc_start: 0.8008 (t0) cc_final: 0.7278 (t70) REVERT: C 51 MET cc_start: 0.4845 (ttm) cc_final: 0.4141 (mtm) REVERT: C 81 TYR cc_start: 0.8517 (m-80) cc_final: 0.8194 (m-80) REVERT: C 106 TYR cc_start: 0.8491 (m-80) cc_final: 0.8096 (m-80) REVERT: C 150 TYR cc_start: 0.8115 (m-80) cc_final: 0.7884 (m-80) REVERT: C 183 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7483 (pptt) REVERT: C 229 ASP cc_start: 0.8319 (m-30) cc_final: 0.7860 (m-30) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.9246 time to fit residues: 124.6698 Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 105 ASP 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131148 restraints weight = 7159.579| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.42 r_work: 0.3186 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7179 Z= 0.244 Angle : 0.626 10.082 9633 Z= 0.295 Chirality : 0.042 0.158 960 Planarity : 0.005 0.044 1050 Dihedral : 21.043 177.841 2091 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.94 % Allowed : 14.56 % 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: 1.64 (0.32), residues: 714 helix: 1.84 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.034 0.002 PHE A 144 TYR 0.034 0.002 TYR C 177 ARG 0.006 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 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.624 Fit side-chains REVERT: A 21 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.6901 (t70) REVERT: A 183 LYS cc_start: 0.7398 (pttt) cc_final: 0.7061 (pptt) REVERT: B 106 TYR cc_start: 0.8496 (m-80) cc_final: 0.8219 (m-80) REVERT: B 170 MET cc_start: 0.8317 (mtt) cc_final: 0.8005 (mtt) REVERT: B 171 ARG cc_start: 0.7635 (mtm110) cc_final: 0.6880 (ttm-80) REVERT: B 183 LYS cc_start: 0.7682 (pttt) cc_final: 0.7321 (pptt) REVERT: B 186 ARG cc_start: 0.7691 (ttt90) cc_final: 0.7365 (ttt90) REVERT: B 229 ASP cc_start: 0.8360 (m-30) cc_final: 0.7931 (m-30) REVERT: C 21 ASP cc_start: 0.8002 (t0) cc_final: 0.7290 (t70) REVERT: C 51 MET cc_start: 0.4775 (ttm) cc_final: 0.4067 (mtm) REVERT: C 81 TYR cc_start: 0.8707 (m-80) cc_final: 0.8404 (m-80) REVERT: C 106 TYR cc_start: 0.8488 (m-80) cc_final: 0.8040 (m-80) REVERT: C 183 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7470 (pptt) REVERT: C 229 ASP cc_start: 0.8337 (m-30) cc_final: 0.7855 (m-30) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.9248 time to fit residues: 121.5098 Evaluate side-chains 129 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 105 ASP 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: 0.6980 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130348 restraints weight = 7162.267| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.39 r_work: 0.3232 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 0.037 7179 Z= 0.217 Angle : 0.616 9.796 9633 Z= 0.293 Chirality : 0.041 0.155 960 Planarity : 0.005 0.044 1050 Dihedral : 20.464 170.848 2091 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.10 % Allowed : 15.37 % 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: 1.71 (0.32), residues: 714 helix: 1.89 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.16 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 42 HIS 0.002 0.001 HIS B 172 PHE 0.035 0.002 PHE A 144 TYR 0.032 0.001 TYR B 177 ARG 0.007 0.001 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.38 seconds wall clock time: 77 minutes 28.14 seconds (4648.14 seconds total)