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/8dat_27275.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.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=3.8 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.map" } resolution = 3.8 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= 3.872 sd= 7.650 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 1 5.16 5 C 375 2.51 5 N 105 2.21 5 O 120 1.98 5 H 625 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: 1226 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1226 Classifications: {'peptide': 76} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 0.65, per 1000 atoms: 0.53 Number of scatterers: 1226 At special positions: 0 Unit cell: (47.88, 43.624, 42.56, 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 1 16.00 O 120 8.00 N 105 7.00 C 375 6.00 H 625 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: 0.31 Conformation dependent library (CDL) restraints added in 43.0 milliseconds 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 0.38 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: 625 1.14 - 1.31: 107 1.31 - 1.47: 210 1.47 - 1.64: 287 1.64 - 1.80: 2 Bond restraints: 1231 Sorted by residual: bond pdb=" N GLY K 247 " pdb=" H GLY K 247 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" N LYS K 227 " pdb=" H LYS K 227 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" NH2 ARG K 274 " pdb="HH21 ARG K 274 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG K 274 " pdb="HH22 ARG K 274 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS K 229 " pdb=" H LYS K 229 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 1226 not shown) Histogram of bond angle deviations from ideal: 101.02 - 107.06: 17 107.06 - 113.11: 1536 113.11 - 119.15: 239 119.15 - 125.19: 439 125.19 - 131.23: 10 Bond angle restraints: 2241 Sorted by residual: angle pdb=" N ASN K 260 " pdb=" CA ASN K 260 " pdb=" CB ASN K 260 " ideal model delta sigma weight residual 112.63 110.95 1.68 1.61e+00 3.86e-01 1.08e+00 angle pdb=" C ILE K 236 " pdb=" N PRO K 237 " pdb=" CA PRO K 237 " ideal model delta sigma weight residual 119.66 120.42 -0.76 7.30e-01 1.88e+00 1.08e+00 angle pdb=" N ARG K 274 " pdb=" CA ARG K 274 " pdb=" C ARG K 274 " ideal model delta sigma weight residual 112.54 111.10 1.44 1.51e+00 4.39e-01 9.14e-01 angle pdb=" C PRO K 237 " pdb=" N PRO K 238 " pdb=" CD PRO K 238 " ideal model delta sigma weight residual 125.00 128.84 -3.84 4.10e+00 5.95e-02 8.77e-01 angle pdb=" N GLU K 234 " pdb=" CA GLU K 234 " pdb=" C GLU K 234 " ideal model delta sigma weight residual 114.75 113.61 1.14 1.26e+00 6.30e-01 8.23e-01 ... (remaining 2236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 371 13.88 - 27.76: 31 27.76 - 41.65: 13 41.65 - 55.53: 4 55.53 - 69.41: 3 Dihedral angle restraints: 422 sinusoidal: 329 harmonic: 93 Sorted by residual: dihedral pdb=" N LEU K 215 " pdb=" CA LEU K 215 " pdb=" CB LEU K 215 " pdb=" CG LEU K 215 " ideal model delta sinusoidal sigma weight residual -60.00 -97.18 37.18 3 1.50e+01 4.44e-03 6.48e+00 dihedral pdb=" N MET K 201 " pdb=" CA MET K 201 " pdb=" CB MET K 201 " pdb=" CG MET K 201 " ideal model delta sinusoidal sigma weight residual 60.00 95.58 -35.58 3 1.50e+01 4.44e-03 6.11e+00 dihedral pdb=" CB ARG K 274 " pdb=" CG ARG K 274 " pdb=" CD ARG K 274 " pdb=" NE ARG K 274 " ideal model delta sinusoidal sigma weight residual -60.00 -90.67 30.67 3 1.50e+01 4.44e-03 4.91e+00 ... (remaining 419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 65 0.025 - 0.051: 15 0.051 - 0.076: 8 0.076 - 0.101: 3 0.101 - 0.127: 6 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA ILE K 236 " pdb=" N ILE K 236 " pdb=" C ILE K 236 " pdb=" CB ILE K 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL K 270 " pdb=" N VAL K 270 " pdb=" C VAL K 270 " pdb=" CB VAL K 270 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE K 244 " pdb=" N ILE K 244 " pdb=" C ILE K 244 " pdb=" CB ILE K 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 94 not shown) Planarity restraints: 178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 236 " 0.009 5.00e-02 4.00e+02 1.41e-02 3.20e-01 pdb=" N PRO K 237 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO K 237 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO K 237 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 237 " 0.006 5.00e-02 4.00e+02 8.87e-03 1.26e-01 pdb=" N PRO K 238 " -0.015 5.00e-02 4.00e+02 pdb=" CA PRO K 238 " 0.004 5.00e-02 4.00e+02 pdb=" CD PRO K 238 " 0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 204 " -0.003 2.00e-02 2.50e+03 1.82e-03 9.97e-02 pdb=" CG PHE K 204 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 175 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 148 2.18 - 2.78: 2535 2.78 - 3.39: 3417 3.39 - 3.99: 4574 3.99 - 4.60: 6701 Nonbonded interactions: 17375 Sorted by model distance: nonbonded pdb=" HZ3 LYS K 206 " pdb=" OG1 THR K 212 " model vdw 1.573 1.850 nonbonded pdb=" O GLN K 231 " pdb=" H GLY K 235 " model vdw 1.600 1.850 nonbonded pdb=" OE1 GLU K 218 " pdb=" H GLU K 218 " model vdw 1.638 1.850 nonbonded pdb=" OD1 ASP K 239 " pdb=" H GLN K 240 " model vdw 1.649 1.850 nonbonded pdb=" H ILE K 223 " pdb=" O ARG K 254 " model vdw 1.660 1.850 ... (remaining 17370 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: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.410 Find NCS groups from input model: 0.010 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:1.640 Internal consistency checks: 0.000 Total: 6.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 0.012 606 Z= 0.099 Angle : 0.432 3.840 814 Z= 0.229 Chirality : 0.042 0.127 97 Planarity : 0.002 0.014 105 Dihedral : 10.908 69.410 239 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.45 % Allowed : 8.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.96), residues: 74 helix: 0.35 (1.39), residues: 12 sheet: -2.29 (0.78), residues: 25 loop : 0.88 (1.12), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 272 TYR 0.002 0.001 TYR K 259 PHE 0.005 0.001 PHE K 204 HIS 0.001 0.000 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 606 Z= 0.111 Angle : 0.433 3.960 814 Z= 0.213 Chirality : 0.051 0.141 97 Planarity : 0.003 0.019 105 Dihedral : 10.927 79.275 239 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.45 % Allowed : 5.80 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (1.00), residues: 74 helix: 1.58 (1.81), residues: 12 sheet: -2.24 (0.78), residues: 25 loop : 0.96 (1.10), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 272 TYR 0.001 0.000 TYR K 259 PHE 0.002 0.001 PHE K 245 HIS 0.002 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 8.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 606 Z= 0.116 Angle : 0.454 4.300 814 Z= 0.226 Chirality : 0.052 0.144 97 Planarity : 0.003 0.021 105 Dihedral : 10.590 65.684 239 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.90 % Allowed : 7.25 % Favored : 89.86 % 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: -1.42 (0.90), residues: 74 helix: -0.77 (1.24), residues: 18 sheet: -1.82 (0.94), residues: 18 loop : -0.38 (0.97), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 272 TYR 0.001 0.001 TYR K 259 PHE 0.005 0.001 PHE K 204 HIS 0.001 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 5.0317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 606 Z= 0.075 Angle : 0.399 3.997 814 Z= 0.188 Chirality : 0.051 0.147 97 Planarity : 0.003 0.022 105 Dihedral : 10.342 59.721 239 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.45 % Allowed : 7.25 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.95), residues: 74 helix: -0.36 (1.33), residues: 18 sheet: -1.87 (0.93), residues: 18 loop : -0.26 (1.03), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 272 TYR 0.001 0.001 TYR K 259 PHE 0.004 0.001 PHE K 204 HIS 0.001 0.000 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 overall best weight: 7.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 606 Z= 0.098 Angle : 0.418 4.187 814 Z= 0.205 Chirality : 0.051 0.145 97 Planarity : 0.003 0.023 105 Dihedral : 10.067 49.649 239 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.45 % Allowed : 8.70 % Favored : 89.86 % 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: -1.47 (0.90), residues: 74 helix: -0.59 (1.27), residues: 18 sheet: -2.06 (0.91), residues: 18 loop : -0.42 (0.97), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 272 TYR 0.001 0.001 TYR K 259 PHE 0.004 0.001 PHE K 204 HIS 0.001 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 8.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 606 Z= 0.106 Angle : 0.432 4.081 814 Z= 0.213 Chirality : 0.052 0.147 97 Planarity : 0.003 0.021 105 Dihedral : 9.962 48.346 239 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.90 % Allowed : 8.70 % Favored : 88.41 % 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: -1.90 (0.85), residues: 74 helix: -1.25 (1.13), residues: 18 sheet: -2.26 (0.90), residues: 18 loop : -0.56 (0.93), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 272 TYR 0.001 0.001 TYR K 259 PHE 0.006 0.001 PHE K 204 HIS 0.001 0.001 HIS K 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 277.39 seconds wall clock time: 5 minutes 7.75 seconds (307.75 seconds total)