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/8dq0_27645.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.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=3.74 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dq0_27645.pdb" } resolution = 3.74 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= 0.005 sd= 0.378 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 2372 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 14 5.16 5 C 1507 2.51 5 N 440 2.21 5 O 430 1.98 5 H 2362 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 276": "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: 4753 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4753 Classifications: {'peptide': 298} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Time building chain proxies: 1.50, per 1000 atoms: 0.32 Number of scatterers: 4753 At special positions: 0 Unit cell: (63.21, 67.08, 63.21, 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 14 16.00 O 430 8.00 N 440 7.00 C 1507 6.00 H 2362 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: 1.70 Conformation dependent library (CDL) restraints added in 331.4 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 1.96 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: 2353 1.14 - 1.31: 412 1.31 - 1.48: 1000 1.48 - 1.64: 1024 1.64 - 1.81: 19 Bond restraints: 4808 Sorted by residual: bond pdb=" N GLY A 39 " pdb=" H GLY A 39 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N LEU A 277 " pdb=" H LEU A 277 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N ARG A 3 " pdb=" H ARG A 3 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" NH1 ARG A 243 " pdb="HH12 ARG A 243 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N ALA A 6 " pdb=" H ALA A 6 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 4803 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.73: 95 106.73 - 113.54: 5546 113.54 - 120.34: 1581 120.34 - 127.14: 1407 127.14 - 133.95: 46 Bond angle restraints: 8675 Sorted by residual: angle pdb=" C LEU A 78 " pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " ideal model delta sigma weight residual 113.57 109.87 3.70 1.57e+00 4.06e-01 5.55e+00 angle pdb=" C LEU A 77 " pdb=" N LEU A 78 " pdb=" CA LEU A 78 " ideal model delta sigma weight residual 119.83 122.37 -2.54 1.11e+00 8.12e-01 5.23e+00 angle pdb=" CA LEU A 78 " pdb=" C LEU A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 120.58 119.19 1.39 7.40e-01 1.83e+00 3.53e+00 angle pdb=" N PHE A 175 " pdb=" CA PHE A 175 " pdb=" C PHE A 175 " ideal model delta sigma weight residual 109.62 107.26 2.36 1.50e+00 4.44e-01 2.48e+00 angle pdb=" C VAL A 24 " pdb=" N PHE A 25 " pdb=" CA PHE A 25 " ideal model delta sigma weight residual 121.32 118.34 2.98 2.10e+00 2.27e-01 2.01e+00 ... (remaining 8670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1485 17.70 - 35.39: 131 35.39 - 53.09: 44 53.09 - 70.79: 16 70.79 - 88.49: 2 Dihedral angle restraints: 1678 sinusoidal: 1224 harmonic: 454 Sorted by residual: dihedral pdb=" CA THR A 68 " pdb=" C THR A 68 " pdb=" N HIS A 69 " pdb=" CA HIS A 69 " ideal model delta harmonic sigma weight residual -180.00 -164.33 -15.67 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N ARG A 122 " pdb=" CA ARG A 122 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 dihedral pdb=" CA LEU A 4 " pdb=" C LEU A 4 " pdb=" N SER A 5 " pdb=" CA SER A 5 " ideal model delta harmonic sigma weight residual -180.00 -165.10 -14.90 0 5.00e+00 4.00e-02 8.89e+00 ... (remaining 1675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 223 0.027 - 0.055: 92 0.055 - 0.082: 23 0.082 - 0.109: 15 0.109 - 0.136: 5 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE A 154 " pdb=" N ILE A 154 " pdb=" C ILE A 154 " pdb=" CB ILE A 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 355 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 277 " 0.015 5.00e-02 4.00e+02 2.23e-02 7.93e-01 pdb=" N PRO A 278 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 82 " -0.013 5.00e-02 4.00e+02 2.00e-02 6.39e-01 pdb=" N PRO A 83 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO A 124 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.010 5.00e-02 4.00e+02 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 388 2.15 - 2.77: 8752 2.77 - 3.38: 13654 3.38 - 3.99: 18129 3.99 - 4.60: 27252 Nonbonded interactions: 68175 Sorted by model distance: nonbonded pdb="HH11 ARG A 251 " pdb=" OE2 GLU A 256 " model vdw 1.542 1.850 nonbonded pdb=" O ARG A 148 " pdb="HH12 ARG A 171 " model vdw 1.562 1.850 nonbonded pdb=" H LEU A 143 " pdb=" O LEU A 151 " model vdw 1.585 1.850 nonbonded pdb=" O ASP A 44 " pdb=" H VAL A 48 " model vdw 1.591 1.850 nonbonded pdb=" HH TYR A 72 " pdb=" O PHE A 276 " model vdw 1.593 1.850 ... (remaining 68170 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: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.050 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:5.610 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 0.016 2446 Z= 0.114 Angle : 0.502 4.244 3320 Z= 0.266 Chirality : 0.038 0.136 358 Planarity : 0.003 0.022 435 Dihedral : 13.085 70.891 909 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -1.84 (0.45), residues: 296 helix: -0.22 (0.46), residues: 104 sheet: -3.05 (0.65), residues: 41 loop : -1.33 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.009 0.001 TYR A 238 PHE 0.006 0.001 PHE A 276 TRP 0.003 0.000 TRP A 65 HIS 0.002 0.001 HIS A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2446 Z= 0.165 Angle : 0.485 4.104 3320 Z= 0.246 Chirality : 0.051 0.182 358 Planarity : 0.004 0.024 435 Dihedral : 12.214 66.934 909 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: -0.82 (0.50), residues: 296 helix: 1.13 (0.51), residues: 103 sheet: -2.86 (0.74), residues: 48 loop : -0.87 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 150 TYR 0.010 0.002 TYR A 201 PHE 0.007 0.001 PHE A 276 TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2446 Z= 0.209 Angle : 0.518 3.944 3320 Z= 0.267 Chirality : 0.054 0.171 358 Planarity : 0.004 0.031 435 Dihedral : 11.815 59.003 909 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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: -0.96 (0.48), residues: 296 helix: 0.76 (0.51), residues: 98 sheet: -2.61 (0.85), residues: 38 loop : -0.98 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.011 0.002 TYR A 201 PHE 0.007 0.002 PHE A 276 TRP 0.008 0.002 TRP A 49 HIS 0.004 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2446 Z= 0.162 Angle : 0.467 4.022 3320 Z= 0.238 Chirality : 0.051 0.203 358 Planarity : 0.003 0.023 435 Dihedral : 11.560 56.847 909 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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: -0.87 (0.49), residues: 296 helix: 0.85 (0.51), residues: 99 sheet: -2.51 (0.85), residues: 38 loop : -0.96 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.009 0.002 TYR A 201 PHE 0.008 0.001 PHE A 276 TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 20.0000 chunk 27 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.1584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2446 Z= 0.114 Angle : 0.417 3.925 3320 Z= 0.209 Chirality : 0.049 0.192 358 Planarity : 0.003 0.023 435 Dihedral : 11.003 53.918 909 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.59 (0.50), residues: 296 helix: 1.05 (0.52), residues: 99 sheet: -2.34 (0.86), residues: 38 loop : -0.76 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.007 0.001 TYR A 201 PHE 0.007 0.001 PHE A 276 TRP 0.005 0.001 TRP A 49 HIS 0.003 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2446 Z= 0.074 Angle : 0.385 3.893 3320 Z= 0.189 Chirality : 0.047 0.190 358 Planarity : 0.003 0.022 435 Dihedral : 10.278 50.572 909 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: -0.09 (0.51), residues: 296 helix: 1.47 (0.53), residues: 99 sheet: -2.01 (0.92), residues: 38 loop : -0.49 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.006 0.001 TYR A 238 PHE 0.006 0.001 PHE A 276 TRP 0.004 0.001 TRP A 129 HIS 0.003 0.001 HIS A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 569.07 seconds wall clock time: 9 minutes 58.58 seconds (598.58 seconds total)