Starting phenix.real_space_refine on Mon Jun 24 12:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnw_37674/06_2024/8wnw_37674_updated.pdb" } resolution = 3.5 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= 0.001 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: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 6 5.16 5 C 909 2.51 5 N 220 2.21 5 O 263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 1400 Number of models: 1 Model: "" Number of chains: 2 Chain: "Q" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1251 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "Q" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 149 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.46, per 1000 atoms: 1.76 Number of scatterers: 1400 At special positions: 0 Unit cell: (57.2023, 68.6427, 59.2823, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 Mg 2 11.99 O 263 8.00 N 220 7.00 C 909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 281.4 milliseconds 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 0 sheets defined 63.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'Q' and resid 92 through 123 removed outlier: 3.546A pdb=" N VAL Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) Proline residue: Q 112 - end of helix Processing helix chain 'Q' and resid 131 through 163 removed outlier: 4.371A pdb=" N THR Q 143 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR Q 144 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA Q 162 " --> pdb=" O ASN Q 158 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA Q 163 " --> pdb=" O GLY Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 203 removed outlier: 4.285A pdb=" N SER Q 185 " --> pdb=" O SER Q 182 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Q 200 " --> pdb=" O VAL Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 227 82 hydrogen bonds defined for protein. 195 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: 0.32 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 506 1.39 - 1.56: 910 1.56 - 1.74: 0 1.74 - 1.92: 9 1.92 - 2.09: 8 Bond restraints: 1433 Sorted by residual: bond pdb=" C10 LMG Q 301 " pdb=" O7 LMG Q 301 " ideal model delta sigma weight residual 1.336 1.457 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C28 LMG Q 301 " pdb=" O8 LMG Q 301 " ideal model delta sigma weight residual 1.331 1.447 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" N ASN Q 228 " pdb=" CA ASN Q 228 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 2.02e+01 bond pdb=" N VAL Q 187 " pdb=" CA VAL Q 187 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" C ASN Q 228 " pdb=" N PRO Q 229 " ideal model delta sigma weight residual 1.329 1.364 -0.034 1.18e-02 7.18e+03 8.49e+00 ... (remaining 1428 not shown) Histogram of bond angle deviations from ideal: 84.51 - 100.45: 8 100.45 - 116.39: 968 116.39 - 132.33: 979 132.33 - 148.27: 5 148.27 - 164.21: 4 Bond angle restraints: 1964 Sorted by residual: angle pdb=" C TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta sigma weight residual 109.34 118.47 -9.13 1.55e+00 4.16e-01 3.47e+01 angle pdb=" NB CLA Q 302 " pdb="MG CLA Q 302 " pdb=" ND CLA Q 302 " ideal model delta sigma weight residual 176.90 161.19 15.71 3.00e+00 1.11e-01 2.74e+01 angle pdb=" NB CLA Q 303 " pdb="MG CLA Q 303 " pdb=" ND CLA Q 303 " ideal model delta sigma weight residual 176.90 162.26 14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" N THR Q 143 " pdb=" CA THR Q 143 " pdb=" C THR Q 143 " ideal model delta sigma weight residual 111.07 105.96 5.11 1.07e+00 8.73e-01 2.28e+01 angle pdb=" CA PRO Q 85 " pdb=" C PRO Q 85 " pdb=" O PRO Q 85 " ideal model delta sigma weight residual 121.56 116.19 5.37 1.16e+00 7.43e-01 2.14e+01 ... (remaining 1959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.54: 753 14.54 - 29.08: 68 29.08 - 43.62: 14 43.62 - 58.16: 12 58.16 - 72.69: 2 Dihedral angle restraints: 849 sinusoidal: 352 harmonic: 497 Sorted by residual: dihedral pdb=" C TYR Q 141 " pdb=" N TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR Q 98 " pdb=" N THR Q 98 " pdb=" CA THR Q 98 " pdb=" CB THR Q 98 " ideal model delta harmonic sigma weight residual -122.00 -132.91 10.91 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta harmonic sigma weight residual 122.80 131.99 -9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 846 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.083: 123 0.083 - 0.166: 74 0.166 - 0.248: 18 0.248 - 0.331: 3 0.331 - 0.413: 1 Chirality restraints: 219 Sorted by residual: chirality pdb=" CA TYR Q 141 " pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CB TYR Q 141 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA THR Q 98 " pdb=" N THR Q 98 " pdb=" C THR Q 98 " pdb=" CB THR Q 98 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU Q 154 " pdb=" N LEU Q 154 " pdb=" C LEU Q 154 " pdb=" CB LEU Q 154 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 216 not shown) Planarity restraints: 249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CLA Q 302 " 0.070 2.00e-02 2.50e+03 1.30e-01 2.11e+02 pdb=" ND CLA Q 302 " 0.067 2.00e-02 2.50e+03 pdb=" NA CLA Q 302 " 0.062 2.00e-02 2.50e+03 pdb=" NC CLA Q 302 " 0.060 2.00e-02 2.50e+03 pdb="MG CLA Q 302 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA Q 303 " -0.073 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" ND CLA Q 303 " -0.071 2.00e-02 2.50e+03 pdb=" NA CLA Q 303 " -0.048 2.00e-02 2.50e+03 pdb=" NC CLA Q 303 " -0.045 2.00e-02 2.50e+03 pdb="MG CLA Q 303 " 0.236 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA Q 302 " -0.036 2.00e-02 2.50e+03 2.26e-02 6.38e+00 pdb=" C2C CLA Q 302 " 0.024 2.00e-02 2.50e+03 pdb=" C4B CLA Q 302 " 0.021 2.00e-02 2.50e+03 pdb=" CHC CLA Q 302 " -0.015 2.00e-02 2.50e+03 pdb=" NC CLA Q 302 " 0.006 2.00e-02 2.50e+03 ... (remaining 246 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 668 2.98 - 3.46: 1472 3.46 - 3.94: 2366 3.94 - 4.42: 2493 4.42 - 4.90: 3992 Nonbonded interactions: 10991 Sorted by model distance: nonbonded pdb=" C1 CLA Q 302 " pdb=" O1A CLA Q 302 " model vdw 2.500 2.752 nonbonded pdb=" O ALA Q 139 " pdb=" OG1 THR Q 143 " model vdw 2.545 2.440 nonbonded pdb=" N PHE Q 171 " pdb=" O PHE Q 171 " model vdw 2.582 2.496 nonbonded pdb=" N THR Q 87 " pdb=" N GLN Q 88 " model vdw 2.583 2.560 nonbonded pdb=" N LYS Q 170 " pdb=" O LYS Q 170 " model vdw 2.603 2.496 ... (remaining 10986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.930 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 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 : 0.013 0.121 1433 Z= 0.819 Angle : 1.766 15.709 1964 Z= 1.255 Chirality : 0.106 0.413 219 Planarity : 0.013 0.130 249 Dihedral : 13.585 72.693 529 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.31 % Allowed : 8.46 % Favored : 89.23 % Cbeta Deviations : 1.25 % 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: 2.30 (0.65), residues: 169 helix: 2.58 (0.49), residues: 108 sheet: None (None), residues: 0 loop : -0.44 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 223 TYR 0.020 0.003 TYR Q 137 ARG 0.003 0.001 ARG Q 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.148 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8381 (m-30) cc_final: 0.7742 (m-30) REVERT: Q 61 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5849 (tmtt) outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.1839 time to fit residues: 4.9335 Evaluate side-chains 13 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Q 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1433 Z= 0.210 Angle : 0.617 4.895 1964 Z= 0.326 Chirality : 0.040 0.184 219 Planarity : 0.006 0.038 249 Dihedral : 12.513 57.417 247 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 9.23 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.62), residues: 169 helix: 2.10 (0.46), residues: 106 sheet: None (None), residues: 0 loop : -0.13 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE Q 223 TYR 0.009 0.002 TYR Q 137 ARG 0.000 0.000 ARG Q 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.124 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8500 (m-30) cc_final: 0.7782 (m-30) REVERT: Q 61 LYS cc_start: 0.6398 (mmtt) cc_final: 0.5761 (tmtt) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.1253 time to fit residues: 2.5164 Evaluate side-chains 17 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 234 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.0030 chunk 13 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1433 Z= 0.201 Angle : 0.550 5.680 1964 Z= 0.288 Chirality : 0.039 0.144 219 Planarity : 0.005 0.035 249 Dihedral : 12.638 59.100 247 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.08 % Allowed : 12.31 % Favored : 84.62 % 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 (0.62), residues: 169 helix: 1.92 (0.48), residues: 106 sheet: None (None), residues: 0 loop : -0.18 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE Q 233 TYR 0.008 0.001 TYR Q 137 ARG 0.001 0.000 ARG Q 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.138 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8504 (m-30) cc_final: 0.8089 (m-30) REVERT: Q 61 LYS cc_start: 0.6510 (mmtt) cc_final: 0.5799 (tmtt) REVERT: Q 175 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.6043 (pp) outliers start: 4 outliers final: 2 residues processed: 18 average time/residue: 0.1281 time to fit residues: 2.7369 Evaluate side-chains 16 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.0030 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1433 Z= 0.265 Angle : 0.591 4.283 1964 Z= 0.297 Chirality : 0.040 0.159 219 Planarity : 0.005 0.034 249 Dihedral : 12.784 57.264 247 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.08 % Allowed : 14.62 % Favored : 82.31 % 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: 1.19 (0.62), residues: 169 helix: 1.39 (0.48), residues: 107 sheet: None (None), residues: 0 loop : -0.16 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE Q 233 TYR 0.007 0.001 TYR Q 137 ARG 0.002 0.001 ARG Q 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.151 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8525 (m-30) cc_final: 0.8067 (m-30) REVERT: Q 61 LYS cc_start: 0.6696 (mmtt) cc_final: 0.6072 (tmtt) REVERT: Q 175 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6047 (pp) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0917 time to fit residues: 2.6050 Evaluate side-chains 19 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 233 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 1 optimal weight: 0.0870 overall best weight: 0.1116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1433 Z= 0.128 Angle : 0.487 3.710 1964 Z= 0.253 Chirality : 0.038 0.172 219 Planarity : 0.004 0.035 249 Dihedral : 12.752 59.130 247 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.08 % Allowed : 16.92 % Favored : 80.00 % 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 (0.63), residues: 169 helix: 1.85 (0.50), residues: 106 sheet: None (None), residues: 0 loop : -0.13 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE Q 233 TYR 0.017 0.002 TYR Q 133 ARG 0.000 0.000 ARG Q 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.146 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8479 (m-30) cc_final: 0.8036 (m-30) REVERT: Q 61 LYS cc_start: 0.6702 (mmtt) cc_final: 0.5899 (tmtt) REVERT: Q 175 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6130 (pp) REVERT: Q 211 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6866 (tppt) outliers start: 4 outliers final: 1 residues processed: 17 average time/residue: 0.1273 time to fit residues: 2.5961 Evaluate side-chains 16 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 211 LYS Chi-restraints excluded: chain Q residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1433 Z= 0.245 Angle : 0.572 4.043 1964 Z= 0.288 Chirality : 0.040 0.149 219 Planarity : 0.005 0.033 249 Dihedral : 12.848 56.325 247 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 7.69 % Allowed : 14.62 % Favored : 77.69 % 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: 1.22 (0.62), residues: 169 helix: 1.45 (0.48), residues: 107 sheet: None (None), residues: 0 loop : -0.22 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE Q 171 TYR 0.008 0.002 TYR Q 133 ARG 0.002 0.000 ARG Q 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 17 time to evaluate : 0.147 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8527 (m-30) cc_final: 0.8059 (m-30) REVERT: Q 61 LYS cc_start: 0.6515 (mmtt) cc_final: 0.5994 (tmtt) REVERT: Q 175 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6115 (pp) REVERT: Q 211 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6722 (tppt) outliers start: 10 outliers final: 7 residues processed: 25 average time/residue: 0.1091 time to fit residues: 3.2649 Evaluate side-chains 26 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 211 LYS Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 233 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 10 optimal weight: 0.0070 chunk 11 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.1432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Q 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1433 Z= 0.137 Angle : 0.486 3.800 1964 Z= 0.253 Chirality : 0.036 0.132 219 Planarity : 0.004 0.035 249 Dihedral : 12.813 59.915 247 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 6.15 % Allowed : 15.38 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.63), residues: 169 helix: 1.69 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.28 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE Q 233 TYR 0.009 0.001 TYR Q 133 ARG 0.000 0.000 ARG Q 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 15 time to evaluate : 0.146 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8458 (m-30) cc_final: 0.7989 (m-30) REVERT: Q 61 LYS cc_start: 0.6529 (mmtt) cc_final: 0.5916 (tmtt) REVERT: Q 175 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6204 (pp) REVERT: Q 211 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6848 (tppt) outliers start: 8 outliers final: 3 residues processed: 23 average time/residue: 0.1066 time to fit residues: 2.9351 Evaluate side-chains 20 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.0000 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 1 optimal weight: 0.0050 chunk 8 optimal weight: 0.5980 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1433 Z= 0.164 Angle : 0.491 3.861 1964 Z= 0.255 Chirality : 0.036 0.130 219 Planarity : 0.004 0.035 249 Dihedral : 12.830 59.797 247 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 6.15 % Allowed : 15.38 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.63), residues: 169 helix: 1.66 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.42 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE Q 233 TYR 0.010 0.001 TYR Q 133 ARG 0.001 0.000 ARG Q 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.148 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8398 (m-30) cc_final: 0.8096 (m-30) REVERT: Q 61 LYS cc_start: 0.6593 (mmtt) cc_final: 0.5858 (tmtt) REVERT: Q 211 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6777 (tppt) outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 0.1153 time to fit residues: 3.1645 Evaluate side-chains 22 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 211 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.0000 chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 overall best weight: 0.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Q 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1433 Z= 0.156 Angle : 0.491 3.909 1964 Z= 0.255 Chirality : 0.035 0.128 219 Planarity : 0.004 0.035 249 Dihedral : 12.811 59.598 247 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.62 % Allowed : 16.15 % Favored : 79.23 % 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: 1.36 (0.63), residues: 169 helix: 1.68 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.43 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE Q 233 TYR 0.009 0.001 TYR Q 133 ARG 0.000 0.000 ARG Q 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.109 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8386 (m-30) cc_final: 0.8114 (m-30) REVERT: Q 61 LYS cc_start: 0.6597 (mmtt) cc_final: 0.5868 (tmtt) REVERT: Q 211 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6777 (tppt) outliers start: 6 outliers final: 4 residues processed: 19 average time/residue: 0.1138 time to fit residues: 2.5108 Evaluate side-chains 19 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 16 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.0050 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 overall best weight: 0.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1433 Z= 0.128 Angle : 0.467 3.782 1964 Z= 0.243 Chirality : 0.035 0.119 219 Planarity : 0.004 0.035 249 Dihedral : 12.705 58.426 247 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.31 % Allowed : 17.69 % Favored : 80.00 % 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: 1.56 (0.64), residues: 169 helix: 1.82 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -0.28 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE Q 233 TYR 0.009 0.001 TYR Q 133 ARG 0.000 0.000 ARG Q 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.231 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8370 (m-30) cc_final: 0.8093 (m-30) REVERT: Q 61 LYS cc_start: 0.6535 (mmtt) cc_final: 0.5916 (tmtt) outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.1551 time to fit residues: 3.4420 Evaluate side-chains 16 residues out of total 130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 0.0980 chunk 16 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 0.0570 overall best weight: 0.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139128 restraints weight = 1934.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140846 restraints weight = 1219.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142054 restraints weight = 862.734| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1433 Z= 0.115 Angle : 0.463 4.445 1964 Z= 0.246 Chirality : 0.034 0.117 219 Planarity : 0.004 0.036 249 Dihedral : 12.600 58.627 247 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.54 % Allowed : 18.46 % Favored : 80.00 % 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: 1.67 (0.64), residues: 169 helix: 1.88 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -0.18 (0.77), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE Q 233 TYR 0.005 0.001 TYR Q 133 ARG 0.000 0.000 ARG Q 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 909.46 seconds wall clock time: 17 minutes 31.15 seconds (1051.15 seconds total)