Starting phenix.real_space_refine on Sun May 19 16:31:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False resolution=3.07 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ckz_16707.map" } resolution = 3.07 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 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= 0.019 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. 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 18 5.16 5 C 1416 2.51 5 N 389 2.21 5 O 429 1.98 5 H 2261 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 168": "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: 4513 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3342 Inner-chain residues flagged as termini: ['pdbres="VAL A 86 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 212} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1171 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 0.87, per 1000 atoms: 0.19 Number of scatterers: 4513 At special positions: 0 Unit cell: (70.68, 86.49, 99.51, 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 18 16.00 O 429 8.00 N 389 7.00 C 1416 6.00 H 2261 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: 1.14 Conformation dependent library (CDL) restraints added in 151.9 milliseconds Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2257 1.15 - 1.31: 393 1.31 - 1.48: 868 1.48 - 1.65: 1007 1.65 - 1.81: 32 Bond restraints: 4557 Sorted by residual: bond pdb=" ND2 ASN A 5 " pdb="HD22 ASN A 5 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" NE1 TRP A 117 " pdb=" HE1 TRP A 117 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" NE2 GLN A 112 " pdb="HE21 GLN A 112 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N LEU A 189 " pdb=" H LEU A 189 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N PHE A 40 " pdb=" H PHE A 40 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 4552 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.19: 147 107.19 - 113.88: 5515 113.88 - 120.56: 1461 120.56 - 127.25: 1117 127.25 - 133.94: 35 Bond angle restraints: 8275 Sorted by residual: angle pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " ideal model delta sigma weight residual 114.10 117.59 -3.49 2.00e+00 2.50e-01 3.04e+00 angle pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " ideal model delta sigma weight residual 114.10 117.27 -3.17 2.00e+00 2.50e-01 2.52e+00 angle pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " pdb=" CD LYS A 131 " ideal model delta sigma weight residual 111.30 107.72 3.58 2.30e+00 1.89e-01 2.42e+00 angle pdb=" N LYS A 131 " pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " ideal model delta sigma weight residual 110.12 108.02 2.10 1.47e+00 4.63e-01 2.05e+00 angle pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " ideal model delta sigma weight residual 110.28 108.24 2.04 1.55e+00 4.16e-01 1.73e+00 ... (remaining 8270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 1443 17.34 - 34.68: 106 34.68 - 52.02: 42 52.02 - 69.36: 9 69.36 - 86.71: 1 Dihedral angle restraints: 1601 sinusoidal: 1209 harmonic: 392 Sorted by residual: dihedral pdb=" CB MET A 66 " pdb=" CG MET A 66 " pdb=" SD MET A 66 " pdb=" CE MET A 66 " ideal model delta sinusoidal sigma weight residual -60.00 -115.14 55.14 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" CA ALA A 47 " pdb=" C ALA A 47 " pdb=" N THR A 48 " pdb=" CA THR A 48 " ideal model delta harmonic sigma weight residual 180.00 165.05 14.95 0 5.00e+00 4.00e-02 8.94e+00 dihedral pdb=" CA PHE A 32 " pdb=" C PHE A 32 " pdb=" N SER A 33 " pdb=" CA SER A 33 " ideal model delta harmonic sigma weight residual 180.00 165.57 14.43 0 5.00e+00 4.00e-02 8.32e+00 ... (remaining 1598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 237 0.029 - 0.059: 68 0.059 - 0.088: 34 0.088 - 0.118: 11 0.118 - 0.147: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ILE B 153 " pdb=" N ILE B 153 " pdb=" C ILE B 153 " pdb=" CB ILE B 153 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 348 not shown) Planarity restraints: 671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 121 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 122 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 38 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.15e-01 pdb=" N PRO A 49 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.013 5.00e-02 4.00e+02 ... (remaining 668 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 461 2.21 - 2.81: 9076 2.81 - 3.40: 12831 3.40 - 4.00: 16130 4.00 - 4.60: 24029 Nonbonded interactions: 62527 Sorted by model distance: nonbonded pdb=" O HIS A 62 " pdb=" H MET A 66 " model vdw 1.612 1.850 nonbonded pdb=" H ILE A 150 " pdb=" OE2 GLU A 175 " model vdw 1.631 1.850 nonbonded pdb="HE21 GLN B 155 " pdb=" O GLU B 159 " model vdw 1.639 1.850 nonbonded pdb=" H SER B 149 " pdb=" OD2 ASP B 152 " model vdw 1.664 1.850 nonbonded pdb=" OD1 ASN A 195 " pdb=" H CYS A 198 " model vdw 1.665 1.850 ... (remaining 62522 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.790 Find NCS groups from input model: 0.030 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:3.670 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.037 2296 Z= 0.114 Angle : 0.512 4.299 3115 Z= 0.272 Chirality : 0.037 0.147 351 Planarity : 0.004 0.034 406 Dihedral : 11.205 86.706 877 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.95 (0.45), residues: 280 helix: -0.83 (0.34), residues: 187 sheet: -1.70 (1.32), residues: 9 loop : 0.53 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 162 TYR 0.006 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.005 0.001 TRP A 117 HIS 0.001 0.001 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2296 Z= 0.158 Angle : 0.491 4.737 3115 Z= 0.246 Chirality : 0.045 0.172 351 Planarity : 0.005 0.041 406 Dihedral : 10.058 72.293 877 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.50 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -4.31 (0.37), residues: 280 helix: -3.26 (0.26), residues: 187 sheet: -2.70 (0.84), residues: 9 loop : -1.20 (0.53), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.004 0.001 TYR A 145 PHE 0.011 0.002 PHE A 40 TRP 0.004 0.001 TRP A 133 HIS 0.001 0.000 HIS A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2296 Z= 0.218 Angle : 0.530 4.507 3115 Z= 0.266 Chirality : 0.045 0.157 351 Planarity : 0.004 0.036 406 Dihedral : 10.613 72.950 877 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 1.07 % Allowed : 4.64 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.69 (0.34), residues: 280 helix: -4.14 (0.22), residues: 191 sheet: -3.10 (0.68), residues: 9 loop : -2.08 (0.55), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 18 TYR 0.007 0.001 TYR A 164 PHE 0.007 0.002 PHE B 161 TRP 0.006 0.002 TRP A 133 HIS 0.002 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2296 Z= 0.164 Angle : 0.457 4.429 3115 Z= 0.226 Chirality : 0.043 0.152 351 Planarity : 0.004 0.037 406 Dihedral : 10.071 70.574 877 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.71 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.64 (0.33), residues: 280 helix: -4.15 (0.21), residues: 191 sheet: -3.23 (0.60), residues: 9 loop : -1.92 (0.55), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 18 TYR 0.004 0.001 TYR A 164 PHE 0.007 0.001 PHE A 40 TRP 0.005 0.001 TRP A 133 HIS 0.001 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2296 Z= 0.214 Angle : 0.507 4.496 3115 Z= 0.254 Chirality : 0.045 0.155 351 Planarity : 0.004 0.037 406 Dihedral : 10.472 70.235 877 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 2.14 % Allowed : 5.00 % Favored : 92.86 % Rotamer: Outliers : 0.40 % Allowed : 1.62 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -6.01 (0.32), residues: 280 helix: -4.30 (0.20), residues: 190 sheet: -3.47 (0.94), residues: 9 loop : -2.43 (0.55), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR A 164 PHE 0.007 0.001 PHE B 161 TRP 0.006 0.002 TRP A 133 HIS 0.001 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 overall best weight: 8.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2296 Z= 0.195 Angle : 0.472 4.482 3115 Z= 0.237 Chirality : 0.044 0.159 351 Planarity : 0.004 0.037 406 Dihedral : 10.408 70.248 877 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 1.07 % Allowed : 5.71 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.85 (0.33), residues: 280 helix: -4.38 (0.19), residues: 185 sheet: -3.16 (1.35), residues: 9 loop : -2.04 (0.55), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 18 TYR 0.005 0.001 TYR A 164 PHE 0.008 0.002 PHE A 40 TRP 0.005 0.001 TRP A 133 HIS 0.002 0.001 HIS A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 179.21 seconds wall clock time: 3 minutes 37.15 seconds (217.15 seconds total)