Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.2 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.map" } resolution = 3.2 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.007 sd= 0.067 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: 4 Type Number sf(0) Gaussians C 557 2.51 5 N 155 2.21 5 O 180 1.98 5 H 839 0.53 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/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 1731 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1731 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Time building chain proxies: 0.80, per 1000 atoms: 0.46 Number of scatterers: 1731 At special positions: 0 Unit cell: (47.385, 58.968, 57.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 180 8.00 N 155 7.00 C 557 6.00 H 839 1.00 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=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 154.8 milliseconds Finding SS restraints... Secondary structure from input PDB file: 1 helices and 1 sheets defined 2.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.672A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 120 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: 0.45 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.09: 822 1.09 - 1.21: 17 1.21 - 1.32: 146 1.32 - 1.43: 288 1.43 - 1.55: 480 Bond restraints: 1753 Sorted by residual: bond pdb=" N THR A 66 " pdb=" H THR A 66 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" N THR A 106 " pdb=" H THR A 106 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N THR A 40 " pdb=" H THR A 40 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N ALA A 63 " pdb=" H ALA A 63 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N LEU A 109 " pdb=" H LEU A 109 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 1748 not shown) Histogram of bond angle deviations from ideal: 102.78 - 109.02: 831 109.02 - 115.27: 1283 115.27 - 121.51: 582 121.51 - 127.75: 413 127.75 - 134.00: 14 Bond angle restraints: 3123 Sorted by residual: angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 122.37 124.62 -2.25 9.30e-01 1.16e+00 5.83e+00 angle pdb=" N PRO A 64 " pdb=" CA PRO A 64 " pdb=" C PRO A 64 " ideal model delta sigma weight residual 112.47 116.28 -3.81 2.06e+00 2.36e-01 3.42e+00 angle pdb=" N TRP A 108 " pdb=" CA TRP A 108 " pdb=" C TRP A 108 " ideal model delta sigma weight residual 109.23 111.42 -2.19 1.55e+00 4.16e-01 1.99e+00 angle pdb=" N ALA A 63 " pdb=" CA ALA A 63 " pdb=" C ALA A 63 " ideal model delta sigma weight residual 108.76 106.73 2.03 1.44e+00 4.82e-01 1.99e+00 angle pdb=" N GLY A 99 " pdb=" CA GLY A 99 " pdb=" C GLY A 99 " ideal model delta sigma weight residual 113.18 109.94 3.24 2.37e+00 1.78e-01 1.87e+00 ... (remaining 3118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 553 17.44 - 34.87: 54 34.87 - 52.31: 14 52.31 - 69.75: 4 69.75 - 87.19: 1 Dihedral angle restraints: 626 sinusoidal: 426 harmonic: 200 Sorted by residual: dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE A 17 " pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sinusoidal sigma weight residual 60.00 104.31 -44.31 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" CA GLN A 107 " pdb=" C GLN A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta harmonic sigma weight residual -180.00 -166.68 -13.32 0 5.00e+00 4.00e-02 7.10e+00 ... (remaining 623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 76 0.027 - 0.054: 40 0.054 - 0.082: 14 0.082 - 0.109: 4 0.109 - 0.136: 5 Chirality restraints: 139 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL A 97 " pdb=" N VAL A 97 " pdb=" C VAL A 97 " pdb=" CB VAL A 97 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 136 not shown) Planarity restraints: 275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 63 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.71e-01 pdb=" N PRO A 64 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 29 " -0.008 2.00e-02 2.50e+03 4.17e-03 5.21e-01 pdb=" CG PHE A 29 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 29 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 29 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 29 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 63 " 0.003 2.00e-02 2.50e+03 6.34e-03 4.03e-01 pdb=" C ALA A 63 " -0.011 2.00e-02 2.50e+03 pdb=" O ALA A 63 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO A 64 " 0.004 2.00e-02 2.50e+03 ... (remaining 272 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.16: 98 2.16 - 2.75: 2779 2.75 - 3.33: 3985 3.33 - 3.92: 5571 3.92 - 4.50: 7608 Nonbonded interactions: 20041 Sorted by model distance: nonbonded pdb=" OE1 GLN A 24 " pdb=" H GLN A 24 " model vdw 1.578 1.850 nonbonded pdb=" H3 GLY A 16 " pdb=" H ILE A 17 " model vdw 1.629 2.100 nonbonded pdb=" OD1 ASN A 23 " pdb=" HG SER A 27 " model vdw 1.645 1.850 nonbonded pdb=" HG1 THR A 18 " pdb=" O VAL A 31 " model vdw 1.700 1.850 nonbonded pdb=" HG1 THR A 114 " pdb=" O ASN A 118 " model vdw 1.710 1.850 ... (remaining 20036 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.51 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 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: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:2.280 Internal consistency checks: 0.000 Total: 6.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 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 : 0.002 0.018 914 Z= 0.148 Angle : 0.535 3.807 1251 Z= 0.315 Chirality : 0.043 0.136 139 Planarity : 0.003 0.023 158 Dihedral : 11.854 62.010 294 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 1.71 % Allowed : 7.69 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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: -3.04 (0.65), residues: 117 helix: None (None), residues: 0 sheet: -0.99 (0.61), residues: 57 loop : -3.17 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.005 0.001 TYR A 60 PHE 0.011 0.002 PHE A 29 TRP 0.007 0.001 TRP A 92 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 914 Z= 0.209 Angle : 0.519 3.160 1251 Z= 0.296 Chirality : 0.062 0.159 139 Planarity : 0.003 0.019 158 Dihedral : 11.244 53.326 294 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.97 % Favored : 87.18 % Rotamer: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -4.33 (0.62), residues: 117 helix: None (None), residues: 0 sheet: -2.31 (0.48), residues: 72 loop : -3.63 (0.77), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 103 TYR 0.009 0.001 TYR A 96 PHE 0.014 0.003 PHE A 29 TRP 0.008 0.001 TRP A 75 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 914 Z= 0.313 Angle : 0.591 4.819 1251 Z= 0.330 Chirality : 0.064 0.161 139 Planarity : 0.004 0.026 158 Dihedral : 12.857 65.713 294 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 2.56 % Allowed : 11.11 % Favored : 86.32 % Rotamer: Outliers : 4.55 % Allowed : 7.95 % Favored : 87.50 % 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: -4.92 (0.64), residues: 117 helix: None (None), residues: 0 sheet: -2.64 (0.49), residues: 72 loop : -4.11 (0.77), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.012 0.002 TYR A 43 PHE 0.014 0.003 PHE A 29 TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 8.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 914 Z= 0.255 Angle : 0.509 2.635 1251 Z= 0.291 Chirality : 0.062 0.163 139 Planarity : 0.003 0.021 158 Dihedral : 12.510 61.818 294 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 1.71 % Allowed : 10.26 % Favored : 88.03 % Rotamer: Outliers : 4.55 % Allowed : 6.82 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.65), residues: 117 helix: None (None), residues: 0 sheet: -2.84 (0.48), residues: 74 loop : -3.89 (0.84), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 59 TYR 0.009 0.001 TYR A 43 PHE 0.013 0.003 PHE A 29 TRP 0.006 0.001 TRP A 75 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 914 Z= 0.255 Angle : 0.504 3.131 1251 Z= 0.286 Chirality : 0.062 0.162 139 Planarity : 0.003 0.022 158 Dihedral : 12.342 65.473 294 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 2.56 % Allowed : 11.97 % Favored : 85.47 % Rotamer: Outliers : 3.41 % Allowed : 9.09 % Favored : 87.50 % 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: -4.97 (0.68), residues: 117 helix: None (None), residues: 0 sheet: -2.84 (0.49), residues: 74 loop : -3.81 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.011 0.002 TYR A 43 PHE 0.014 0.003 PHE A 29 TRP 0.006 0.001 TRP A 79 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 914 Z= 0.313 Angle : 0.564 3.119 1251 Z= 0.319 Chirality : 0.064 0.171 139 Planarity : 0.003 0.026 158 Dihedral : 13.049 63.925 294 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 3.42 % Allowed : 13.68 % Favored : 82.91 % Rotamer: Outliers : 4.55 % Allowed : 6.82 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.62), residues: 117 helix: None (None), residues: 0 sheet: -2.96 (0.49), residues: 74 loop : -4.24 (0.75), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 103 TYR 0.011 0.002 TYR A 43 PHE 0.014 0.003 PHE A 29 TRP 0.007 0.001 TRP A 75 HIS 0.002 0.001 HIS A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 154.23 seconds wall clock time: 3 minutes 6.28 seconds (186.28 seconds total)