Starting phenix.real_space_refine on Sun May 19 16:31:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False resolution=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map" } resolution = 3.1 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { secondary_structure { enabled = False } c_beta_restraints = 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= 0.011 sd= 0.110 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 S 2 5.16 5 C 894 2.51 5 N 265 2.21 5 O 276 1.98 5 H 1414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 2851 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2851 Classifications: {'peptide': 185} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 179} Time building chain proxies: 0.99, per 1000 atoms: 0.35 Number of scatterers: 2851 At special positions: 0 Unit cell: (62.35, 50.525, 60.2, 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 2 16.00 O 276 8.00 N 265 7.00 C 894 6.00 H 1414 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: 0.76 Conformation dependent library (CDL) restraints added in 100.7 milliseconds 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 1414 1.14 - 1.31: 247 1.31 - 1.47: 588 1.47 - 1.64: 625 1.64 - 1.81: 4 Bond restraints: 2878 Sorted by residual: bond pdb=" N HIS A 169 " pdb=" H HIS A 169 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N ALA A 174 " pdb=" H ALA A 174 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N PHE A 146 " pdb=" H PHE A 146 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" ND2 ASN A 98 " pdb="HD22 ASN A 98 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N ALA A 178 " pdb=" H ALA A 178 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 2873 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.01: 62 107.01 - 113.09: 3324 113.09 - 119.16: 571 119.16 - 125.23: 1123 125.23 - 131.31: 106 Bond angle restraints: 5186 Sorted by residual: angle pdb=" N LEU A 107 " pdb=" CA LEU A 107 " pdb=" C LEU A 107 " ideal model delta sigma weight residual 109.96 106.61 3.35 1.58e+00 4.01e-01 4.50e+00 angle pdb=" N GLY A 136 " pdb=" CA GLY A 136 " pdb=" C GLY A 136 " ideal model delta sigma weight residual 113.18 109.07 4.11 2.37e+00 1.78e-01 3.00e+00 angle pdb=" N ALA A 105 " pdb=" CA ALA A 105 " pdb=" C ALA A 105 " ideal model delta sigma weight residual 107.91 111.43 -3.52 2.05e+00 2.38e-01 2.96e+00 angle pdb=" N GLY A 125 " pdb=" CA GLY A 125 " pdb=" C GLY A 125 " ideal model delta sigma weight residual 113.18 110.03 3.15 2.37e+00 1.78e-01 1.76e+00 angle pdb=" CA GLU A 109 " pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " ideal model delta sigma weight residual 114.10 116.73 -2.63 2.00e+00 2.50e-01 1.73e+00 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 902 15.01 - 30.02: 62 30.02 - 45.02: 29 45.02 - 60.03: 15 60.03 - 75.04: 2 Dihedral angle restraints: 1010 sinusoidal: 733 harmonic: 277 Sorted by residual: dihedral pdb=" CA PRO A 106 " pdb=" C PRO A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU A 109 " pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " ideal model delta sinusoidal sigma weight residual -180.00 -121.53 -58.47 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 107 0.025 - 0.050: 74 0.050 - 0.075: 19 0.075 - 0.099: 11 0.099 - 0.124: 14 Chirality restraints: 225 Sorted by residual: chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 160 " pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CB ILE A 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE A 70 " pdb=" N ILE A 70 " pdb=" C ILE A 70 " pdb=" CB ILE A 70 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 222 not shown) Planarity restraints: 441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 105 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 106 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 168 " -0.005 2.00e-02 2.50e+03 9.68e-03 9.38e-01 pdb=" C SER A 168 " 0.017 2.00e-02 2.50e+03 pdb=" O SER A 168 " -0.006 2.00e-02 2.50e+03 pdb=" N HIS A 169 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 121 " -0.015 5.00e-02 4.00e+02 2.24e-02 7.99e-01 pdb=" N PRO A 122 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.012 5.00e-02 4.00e+02 ... (remaining 438 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 258 2.18 - 2.78: 5401 2.78 - 3.39: 7486 3.39 - 3.99: 10573 3.99 - 4.60: 15217 Nonbonded interactions: 38935 Sorted by model distance: nonbonded pdb=" HG1 THR A 22 " pdb=" OD2 ASP A 78 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASN A 76 " pdb=" HH TYR A 138 " model vdw 1.593 1.850 nonbonded pdb=" O SER A 119 " pdb=" H ARG A 121 " model vdw 1.600 1.850 nonbonded pdb=" OG1 THR A 132 " pdb=" HG SER A 168 " model vdw 1.619 1.850 nonbonded pdb="HD21 ASN A 76 " pdb=" HD1 PHE A 146 " model vdw 1.700 2.100 ... (remaining 38930 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=0.49 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: 0.030 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 6.620 Find NCS groups from input model: 0.030 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.900 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.003 0.025 1464 Z= 0.139 Angle : 0.564 4.108 1981 Z= 0.312 Chirality : 0.044 0.124 225 Planarity : 0.004 0.048 262 Dihedral : 11.089 72.094 532 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 1.30 % Allowed : 3.90 % Favored : 94.81 % 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: -3.98 (0.51), residues: 183 helix: -2.70 (0.49), residues: 66 sheet: -1.01 (0.69), residues: 51 loop : -3.78 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.009 0.002 TYR A 138 PHE 0.005 0.001 PHE A 100 HIS 0.003 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1464 Z= 0.134 Angle : 0.545 3.756 1981 Z= 0.288 Chirality : 0.056 0.152 225 Planarity : 0.004 0.033 262 Dihedral : 11.198 69.602 532 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.81 % 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: -3.09 (0.54), residues: 183 helix: -1.73 (0.55), residues: 66 sheet: -0.37 (0.73), residues: 51 loop : -3.72 (0.54), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.009 0.002 TYR A 126 PHE 0.004 0.001 PHE A 100 HIS 0.004 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1464 Z= 0.107 Angle : 0.473 3.466 1981 Z= 0.249 Chirality : 0.054 0.141 225 Planarity : 0.004 0.032 262 Dihedral : 11.141 69.301 532 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.95 % Allowed : 3.90 % Favored : 94.16 % 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: -2.60 (0.58), residues: 183 helix: -0.97 (0.63), residues: 66 sheet: -0.73 (0.66), residues: 61 loop : -3.66 (0.62), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.008 0.001 TYR A 138 PHE 0.004 0.001 PHE A 58 HIS 0.003 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1464 Z= 0.128 Angle : 0.529 3.761 1981 Z= 0.277 Chirality : 0.056 0.152 225 Planarity : 0.004 0.025 262 Dihedral : 11.560 70.377 532 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.60 % Allowed : 5.84 % Favored : 91.56 % 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: -2.37 (0.58), residues: 183 helix: -0.79 (0.63), residues: 65 sheet: -0.58 (0.66), residues: 61 loop : -3.51 (0.61), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.006 0.001 TYR A 126 PHE 0.004 0.001 PHE A 100 HIS 0.006 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1464 Z= 0.138 Angle : 0.523 3.876 1981 Z= 0.276 Chirality : 0.056 0.140 225 Planarity : 0.004 0.027 262 Dihedral : 12.070 71.767 532 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.25 % Allowed : 7.14 % Favored : 89.61 % 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: -2.31 (0.59), residues: 183 helix: -0.60 (0.65), residues: 66 sheet: -0.69 (0.65), residues: 61 loop : -3.53 (0.63), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.008 0.002 TYR A 126 PHE 0.005 0.001 PHE A 58 HIS 0.005 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1464 Z= 0.103 Angle : 0.481 3.606 1981 Z= 0.251 Chirality : 0.055 0.149 225 Planarity : 0.004 0.027 262 Dihedral : 11.718 73.041 532 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.25 % Allowed : 7.79 % Favored : 88.96 % 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: -2.13 (0.58), residues: 183 helix: -0.32 (0.65), residues: 66 sheet: -0.18 (0.75), residues: 49 loop : -3.54 (0.54), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.007 0.001 TYR A 138 PHE 0.004 0.001 PHE A 58 HIS 0.004 0.001 HIS A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 443.73 seconds wall clock time: 7 minutes 56.64 seconds (476.64 seconds total)