Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.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=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi4_43248.map" } resolution = 3.1 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= 0.016 sd= 0.077 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 None 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: 1.63, per 1000 atoms: 0.33 Number of scatterers: 4942 At special positions: 0 Unit cell: (61.694, 58.864, 63.392, 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: 2.18 Conformation dependent library (CDL) restraints added in 280.9 milliseconds Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.4% alpha, 0.0% 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 11 through 30 removed outlier: 3.599A pdb=" N PHE A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 35 through 65 removed outlier: 4.006A pdb=" N ARG A 38 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 65 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 79 through 99 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 102 through 123 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 146 Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 163 through 191 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 195 through 218 removed outlier: 4.264A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.709A pdb=" N VAL A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 248 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.984A pdb=" N PHE A 262 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 178 hydrogen bonds defined for protein. 309 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: 1.69 Time building geometry restraints manager: 2.37 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 256 " pdb=" H GLY A 256 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" N LEU A 92 " pdb=" H LEU A 92 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N PHE A 14 " pdb=" H PHE A 14 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.58e+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 6.56e+01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 157 107.23 - 113.92: 5714 113.92 - 120.61: 1939 120.61 - 127.30: 1232 127.30 - 133.98: 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 112.64 110.72 1.92 1.21e+00 6.83e-01 2.51e+00 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 109.34 106.53 2.81 2.08e+00 2.31e-01 1.82e+00 angle pdb=" N PHE A 28 " pdb=" CA PHE A 28 " pdb=" C PHE A 28 " ideal model delta sigma weight residual 112.54 111.06 1.48 1.22e+00 6.72e-01 1.47e+00 angle pdb=" C ILE A 86 " pdb=" N PRO A 87 " pdb=" CD PRO A 87 " ideal model delta sigma weight residual 125.00 129.58 -4.58 4.10e+00 5.95e-02 1.25e+00 angle pdb=" C ILE A 16 " pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 125.00 129.54 -4.54 4.10e+00 5.95e-02 1.23e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 1596 14.24 - 28.47: 129 28.47 - 42.71: 40 42.71 - 56.94: 37 56.94 - 71.17: 7 Dihedral angle restraints: 1809 sinusoidal: 1211 harmonic: 598 Sorted by residual: 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 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+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 -107.39 47.39 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " pdb=" CD GLU A 134 " pdb=" OE1 GLU A 134 " ideal model delta sinusoidal sigma weight residual 0.00 -71.17 71.17 1 3.00e+01 1.11e-03 7.22e+00 ... (remaining 1806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 225 0.022 - 0.044: 93 0.044 - 0.066: 26 0.066 - 0.088: 33 0.088 - 0.109: 13 Chirality restraints: 390 Sorted by residual: 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 2.99e-01 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 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 102 " pdb=" N PRO A 102 " pdb=" C PRO A 102 " pdb=" CB PRO A 102 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.39e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 206 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 207 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 45 " -0.005 2.00e-02 2.50e+03 9.52e-03 9.07e-01 pdb=" C GLY A 45 " 0.016 2.00e-02 2.50e+03 pdb=" O GLY A 45 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE A 46 " -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 9.42e-03 8.87e-01 pdb=" C LEU A 44 " 0.016 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.005 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 358 2.14 - 2.75: 8692 2.75 - 3.37: 15112 3.37 - 3.98: 19734 3.98 - 4.60: 29848 Nonbonded interactions: 73744 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.523 1.850 nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.568 1.850 nonbonded pdb=" HE1 TRP A 258 " pdb=" OG1 THR A 302 " model vdw 1.574 1.850 nonbonded pdb=" O TRP A 258 " pdb=" HG SER A 261 " model vdw 1.584 1.850 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.589 1.850 ... (remaining 73739 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: 0.040 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: 0.050 Extract box with map and model: 0.370 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.620 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:6.810 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 0.014 2534 Z= 0.120 Angle : 0.437 4.582 3457 Z= 0.234 Chirality : 0.035 0.109 390 Planarity : 0.004 0.028 420 Dihedral : 11.297 71.175 856 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.78 % Allowed : 0.00 % Favored : 99.22 % 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: -1.31 (0.49), residues: 306 helix: -0.82 (0.33), residues: 244 sheet: None (None), residues: 0 loop : -0.21 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.009 0.001 TYR A 304 PHE 0.008 0.001 PHE A 34 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 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: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1312 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= 0.243 Angle : 0.443 4.589 3457 Z= 0.230 Chirality : 0.042 0.185 390 Planarity : 0.004 0.026 420 Dihedral : 10.474 59.580 856 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.48 % Favored : 90.20 % Rotamer: Outliers : 0.78 % Allowed : 0.78 % 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: -2.99 (0.44), residues: 306 helix: -1.83 (0.29), residues: 244 sheet: None (None), residues: 0 loop : -1.62 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.007 0.001 TYR A 304 PHE 0.010 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2534 Z= 0.352 Angle : 0.488 4.883 3457 Z= 0.257 Chirality : 0.045 0.204 390 Planarity : 0.005 0.031 420 Dihedral : 10.783 52.206 856 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.46 % Favored : 88.89 % Rotamer: Outliers : 0.78 % Allowed : 1.96 % Favored : 97.25 % 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: -3.61 (0.41), residues: 306 helix: -2.09 (0.28), residues: 241 sheet: None (None), residues: 0 loop : -2.70 (0.67), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 198 TYR 0.008 0.001 TYR A 304 PHE 0.011 0.001 PHE A 34 TRP 0.007 0.001 TRP A 247 HIS 0.001 0.001 HIS A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2534 Z= 0.357 Angle : 0.468 4.837 3457 Z= 0.246 Chirality : 0.044 0.178 390 Planarity : 0.005 0.031 420 Dihedral : 10.378 51.310 856 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.78 % Favored : 88.56 % Rotamer: Outliers : 0.78 % Allowed : 1.57 % Favored : 97.65 % 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: -3.53 (0.41), residues: 306 helix: -2.05 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -2.58 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.007 0.001 TYR A 61 PHE 0.011 0.001 PHE A 34 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 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: 10.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2534 Z= 0.354 Angle : 0.480 4.818 3457 Z= 0.252 Chirality : 0.045 0.192 390 Planarity : 0.005 0.031 420 Dihedral : 10.528 50.510 856 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.46 % Favored : 88.56 % Rotamer: Outliers : 0.78 % Allowed : 2.75 % Favored : 96.47 % 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: -3.63 (0.41), residues: 306 helix: -2.12 (0.28), residues: 244 sheet: None (None), residues: 0 loop : -2.64 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.006 0.001 TYR A 61 PHE 0.010 0.001 PHE A 34 TRP 0.007 0.001 TRP A 247 HIS 0.001 0.001 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2534 Z= 0.342 Angle : 0.467 4.813 3457 Z= 0.245 Chirality : 0.044 0.181 390 Planarity : 0.005 0.030 420 Dihedral : 10.353 50.267 856 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.11 % Favored : 88.56 % Rotamer: Outliers : 0.78 % Allowed : 1.96 % Favored : 97.25 % 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: -3.52 (0.41), residues: 306 helix: -2.06 (0.28), residues: 244 sheet: None (None), residues: 0 loop : -2.53 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.006 0.001 TYR A 61 PHE 0.011 0.001 PHE A 34 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 196.96 seconds wall clock time: 3 minutes 54.99 seconds (234.99 seconds total)