Starting phenix.real_space_refine on Sun May 19 16:32:00 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=False secondary_structure.enabled=True 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 { 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= 0.005 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: 0.01s 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: 1.72, per 1000 atoms: 0.36 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: 2.20 Conformation dependent library (CDL) restraints added in 328.4 milliseconds Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 40.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.477A pdb=" N GLU A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 72 through 81 removed outlier: 6.190A pdb=" N LEU A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.506A pdb=" N GLN A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.598A pdb=" N ARG A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.153A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.067A pdb=" N VAL A 90 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 137 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA A 92 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TRP A 34 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP A 65 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 36 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 14 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 16 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLN A 9 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.637A pdb=" N PHE A 166 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU A 151 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU A 144 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 153 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP A 142 " --> pdb=" O VAL A 153 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 2.13 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: 311 2.15 - 2.77: 8743 2.77 - 3.38: 13568 3.38 - 3.99: 17941 3.99 - 4.60: 27182 Nonbonded interactions: 67745 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 67740 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: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.040 Extract box with map and model: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 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:6.600 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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= 0.149 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 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 25 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2446 Z= 0.286 Angle : 0.521 3.944 3320 Z= 0.268 Chirality : 0.052 0.217 358 Planarity : 0.004 0.026 435 Dihedral : 12.219 65.220 909 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 1.69 % Allowed : 6.76 % Favored : 91.55 % Rotamer: Outliers : 0.40 % Allowed : 3.59 % Favored : 96.02 % 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: -4.13 (0.39), residues: 296 helix: -1.45 (0.44), residues: 103 sheet: -4.14 (0.59), residues: 51 loop : -3.17 (0.37), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.012 0.002 TYR A 201 PHE 0.009 0.002 PHE A 25 TRP 0.007 0.001 TRP A 34 HIS 0.005 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2446 Z= 0.398 Angle : 0.578 4.022 3320 Z= 0.302 Chirality : 0.055 0.200 358 Planarity : 0.004 0.025 435 Dihedral : 12.657 64.695 909 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 2.36 % Allowed : 12.50 % Favored : 85.14 % Rotamer: Outliers : 1.59 % Allowed : 6.37 % Favored : 92.03 % 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: -5.30 (0.34), residues: 296 helix: -2.21 (0.42), residues: 97 sheet: -4.39 (0.55), residues: 41 loop : -4.28 (0.32), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 28 TYR 0.011 0.002 TYR A 201 PHE 0.010 0.002 PHE A 276 TRP 0.009 0.002 TRP A 142 HIS 0.004 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2446 Z= 0.353 Angle : 0.548 4.072 3320 Z= 0.285 Chirality : 0.055 0.227 358 Planarity : 0.004 0.024 435 Dihedral : 12.685 65.764 909 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 3.04 % Allowed : 11.82 % Favored : 85.14 % Rotamer: Outliers : 1.99 % Allowed : 7.97 % Favored : 90.04 % 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: -5.36 (0.34), residues: 296 helix: -2.36 (0.40), residues: 98 sheet: -4.20 (0.59), residues: 41 loop : -4.33 (0.31), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.011 0.002 TYR A 201 PHE 0.011 0.002 PHE A 276 TRP 0.009 0.002 TRP A 34 HIS 0.005 0.002 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 9.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2446 Z= 0.370 Angle : 0.544 3.936 3320 Z= 0.283 Chirality : 0.054 0.216 358 Planarity : 0.003 0.023 435 Dihedral : 12.789 67.329 909 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 3.72 % Allowed : 12.50 % Favored : 83.78 % Rotamer: Outliers : 2.39 % Allowed : 8.76 % Favored : 88.84 % 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: -5.40 (0.34), residues: 296 helix: -2.31 (0.41), residues: 97 sheet: -4.15 (0.59), residues: 41 loop : -4.42 (0.31), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.011 0.002 TYR A 201 PHE 0.010 0.002 PHE A 276 TRP 0.009 0.002 TRP A 34 HIS 0.004 0.001 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 overall best weight: 9.1998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2446 Z= 0.341 Angle : 0.544 4.195 3320 Z= 0.282 Chirality : 0.054 0.228 358 Planarity : 0.003 0.022 435 Dihedral : 12.955 69.512 909 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 3.72 % Allowed : 13.85 % Favored : 82.43 % Rotamer: Outliers : 3.19 % Allowed : 9.16 % Favored : 87.65 % 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: -5.46 (0.35), residues: 296 helix: -2.35 (0.41), residues: 99 sheet: -4.07 (0.63), residues: 40 loop : -4.55 (0.31), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.011 0.002 TYR A 201 PHE 0.008 0.002 PHE A 276 TRP 0.008 0.002 TRP A 142 HIS 0.005 0.001 HIS A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 209.99 seconds wall clock time: 4 minutes 5.88 seconds (245.88 seconds total)