Starting phenix.real_space_refine on Sun May 19 16:31:30 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.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=3.2 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.pdb" } resolution = 3.2 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= 0.015 sd= 0.069 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 9 5.16 5 C 1662 2.51 5 N 380 2.21 5 O 402 1.98 5 H 2489 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "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: 4942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4942 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 1.48, per 1000 atoms: 0.30 Number of scatterers: 4942 At special positions: 0 Unit cell: (62.826, 60.562, 62.826, 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 9 16.00 O 402 8.00 N 380 7.00 C 1662 6.00 H 2489 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: 2.22 Conformation dependent library (CDL) restraints added in 282.6 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2488 1.14 - 1.31: 356 1.31 - 1.48: 1110 1.48 - 1.64: 1052 1.64 - 1.81: 17 Bond restraints: 5023 Sorted by residual: bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N GLY A 263 " pdb=" H GLY A 263 " 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 273 " pdb=" H ALA A 273 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" N ILE A 88 " pdb=" H ILE A 88 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" N ALA A 48 " pdb=" H ALA A 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 192 107.35 - 114.01: 5702 114.01 - 120.66: 1956 120.66 - 127.32: 1192 127.32 - 133.97: 38 Bond angle restraints: 9080 Sorted by residual: angle pdb=" N GLY A 94 " pdb=" CA GLY A 94 " pdb=" C GLY A 94 " ideal model delta sigma weight residual 112.64 110.30 2.34 1.21e+00 6.83e-01 3.74e+00 angle pdb=" C PHE A 260 " pdb=" N SER A 261 " pdb=" CA SER A 261 " ideal model delta sigma weight residual 121.54 124.08 -2.54 1.91e+00 2.74e-01 1.77e+00 angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 110.23 108.85 1.38 1.04e+00 9.25e-01 1.76e+00 angle pdb=" C ALA A 206 " pdb=" CA ALA A 206 " pdb=" CB ALA A 206 " ideal model delta sigma weight residual 113.49 111.21 2.28 1.82e+00 3.02e-01 1.56e+00 angle pdb=" N PRO A 17 " pdb=" CA PRO A 17 " pdb=" C PRO A 17 " ideal model delta sigma weight residual 113.47 111.70 1.77 1.43e+00 4.89e-01 1.54e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 1590 14.32 - 28.64: 133 28.64 - 42.96: 44 42.96 - 57.28: 39 57.28 - 71.60: 3 Dihedral angle restraints: 1809 sinusoidal: 1211 harmonic: 598 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 128.76 51.24 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -108.31 48.31 3 1.50e+01 4.44e-03 8.62e+00 dihedral pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sinusoidal sigma weight residual -60.00 -107.22 47.22 3 1.50e+01 4.44e-03 8.46e+00 ... (remaining 1806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 224 0.023 - 0.046: 102 0.046 - 0.070: 30 0.070 - 0.093: 25 0.093 - 0.116: 9 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA VAL A 43 " pdb=" N VAL A 43 " pdb=" C VAL A 43 " pdb=" CB VAL A 43 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 24 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C SER A 24 " -0.017 2.00e-02 2.50e+03 pdb=" O SER A 24 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A 25 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " -0.005 2.00e-02 2.50e+03 9.83e-03 9.67e-01 pdb=" C LEU A 44 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 22 " -0.005 2.00e-02 2.50e+03 9.66e-03 9.34e-01 pdb=" C ALA A 22 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA A 22 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU A 23 " -0.006 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 594 2.19 - 2.79: 9709 2.79 - 3.40: 14862 3.40 - 4.00: 19485 4.00 - 4.60: 29136 Nonbonded interactions: 73786 Sorted by model distance: nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.592 1.850 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.601 1.850 nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.609 1.850 nonbonded pdb=" O MET A 267 " pdb=" HG SER A 270 " model vdw 1.612 1.850 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.613 1.850 ... (remaining 73781 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=0.50 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: 0.070 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: 0.060 Extract box with map and model: 0.220 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:5.150 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 0.015 2534 Z= 0.097 Angle : 0.440 4.552 3457 Z= 0.242 Chirality : 0.036 0.116 390 Planarity : 0.004 0.023 420 Dihedral : 11.997 71.595 856 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: -0.75 (0.50), residues: 306 helix: -0.55 (0.34), residues: 241 sheet: None (None), residues: 0 loop : 0.49 (0.89), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 198 TYR 0.005 0.001 TYR A 61 PHE 0.007 0.001 PHE A 260 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2534 Z= 0.134 Angle : 0.417 4.743 3457 Z= 0.205 Chirality : 0.041 0.180 390 Planarity : 0.003 0.024 420 Dihedral : 10.933 69.726 856 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.82 % 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: 0.25 (0.48), residues: 306 helix: 0.37 (0.33), residues: 243 sheet: None (None), residues: 0 loop : -0.11 (0.84), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.005 0.001 TYR A 13 PHE 0.006 0.001 PHE A 151 TRP 0.005 0.001 TRP A 177 HIS 0.002 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2534 Z= 0.177 Angle : 0.424 4.907 3457 Z= 0.210 Chirality : 0.043 0.180 390 Planarity : 0.003 0.024 420 Dihedral : 10.402 69.081 856 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.82 % 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: 0.57 (0.48), residues: 306 helix: 0.65 (0.32), residues: 250 sheet: None (None), residues: 0 loop : -0.40 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.006 0.001 TYR A 61 PHE 0.006 0.001 PHE A 133 TRP 0.006 0.001 TRP A 177 HIS 0.002 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2534 Z= 0.148 Angle : 0.394 4.765 3457 Z= 0.193 Chirality : 0.041 0.176 390 Planarity : 0.003 0.024 420 Dihedral : 9.932 72.295 856 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.82 % 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: 1.39 (0.47), residues: 306 helix: 1.13 (0.33), residues: 238 sheet: None (None), residues: 0 loop : 0.52 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.005 0.001 TYR A 61 PHE 0.005 0.001 PHE A 151 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2534 Z= 0.153 Angle : 0.397 4.795 3457 Z= 0.195 Chirality : 0.042 0.176 390 Planarity : 0.003 0.023 420 Dihedral : 9.841 73.980 856 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.39 % Allowed : 1.18 % Favored : 98.43 % 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: 1.52 (0.48), residues: 306 helix: 1.24 (0.34), residues: 238 sheet: None (None), residues: 0 loop : 0.48 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.005 0.001 TYR A 61 PHE 0.006 0.001 PHE A 151 TRP 0.005 0.001 TRP A 177 HIS 0.002 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2534 Z= 0.061 Angle : 0.338 4.561 3457 Z= 0.157 Chirality : 0.038 0.150 390 Planarity : 0.003 0.025 420 Dihedral : 9.172 75.339 856 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.82 % 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: 2.29 (0.49), residues: 306 helix: 1.74 (0.34), residues: 243 sheet: None (None), residues: 0 loop : 0.93 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.004 0.001 TYR A 13 PHE 0.004 0.001 PHE A 151 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 539.34 seconds wall clock time: 9 minutes 37.59 seconds (577.59 seconds total)