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/8esa_28573.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.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=3.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.pdb" } resolution = 3.4 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= 0.770 sd= 7.430 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 72 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 1970 2.51 5 N 563 2.21 5 O 597 1.98 5 H 2957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 63": "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: 6101 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4308 Inner-chain residues flagged as termini: ['pdbres="GLN A 224 "', 'pdbres="THR A 228 "'] Classifications: {'peptide': 273} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1624 Classifications: {'peptide': 99} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 169 Classifications: {'peptide': 12} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 11} Time building chain proxies: 1.93, per 1000 atoms: 0.32 Number of scatterers: 6101 At special positions: 0 Unit cell: (85, 66.3, 68, 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 597 8.00 N 563 7.00 C 1970 6.00 H 2957 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.04 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: 2.21 Conformation dependent library (CDL) restraints added in 338.8 milliseconds Finding SS restraints... Secondary structure from input PDB file: 3 helices and 5 sheets defined 15.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 57 through 84 Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.613A pdb=" N HIS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 174 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.870A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 99 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 96 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 98 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.875A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 214 through 218 Processing sheet with id= D, first strand: chain 'B' and resid 6 through 11 Processing sheet with id= E, first strand: chain 'B' and resid 39 through 41 116 hydrogen bonds defined for protein. 318 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: 1.92 Time building geometry restraints manager: 2.54 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: 2957 1.15 - 1.31: 526 1.31 - 1.48: 1402 1.48 - 1.65: 1284 1.65 - 1.82: 20 Bond restraints: 6189 Sorted by residual: bond pdb=" N MET A 98 " pdb=" H MET A 98 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N VAL A 12 " pdb=" H VAL A 12 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N TYR A 27 " pdb=" H TYR A 27 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N ILE B 92 " pdb=" H ILE B 92 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 127 107.01 - 113.77: 6998 113.77 - 120.52: 2039 120.52 - 127.27: 1871 127.27 - 134.02: 58 Bond angle restraints: 11093 Sorted by residual: angle pdb=" C CYS A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 120.42 117.94 2.48 1.42e+00 4.96e-01 3.06e+00 angle pdb=" N TYR A 159 " pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " ideal model delta sigma weight residual 109.82 112.42 -2.60 1.52e+00 4.33e-01 2.92e+00 angle pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " pdb=" CG TYR A 159 " ideal model delta sigma weight residual 113.90 110.98 2.92 1.80e+00 3.09e-01 2.63e+00 angle pdb=" CA SER A 207 " pdb=" C SER A 207 " pdb=" N PHE A 208 " ideal model delta sigma weight residual 116.84 114.49 2.35 1.71e+00 3.42e-01 1.90e+00 angle pdb=" N ARG A 111 " pdb=" CA ARG A 111 " pdb=" C ARG A 111 " ideal model delta sigma weight residual 108.32 110.54 -2.22 1.64e+00 3.72e-01 1.84e+00 ... (remaining 11088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1948 16.43 - 32.86: 189 32.86 - 49.29: 60 49.29 - 65.72: 26 65.72 - 82.15: 3 Dihedral angle restraints: 2226 sinusoidal: 1552 harmonic: 674 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 dihedral pdb=" CA ARG B 81 " pdb=" CB ARG B 81 " pdb=" CG ARG B 81 " pdb=" CD ARG B 81 " ideal model delta sinusoidal sigma weight residual -60.00 -107.41 47.41 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CA ARG A 256 " pdb=" CB ARG A 256 " pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sinusoidal sigma weight residual -180.00 -134.14 -45.86 3 1.50e+01 4.44e-03 8.24e+00 ... (remaining 2223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 275 0.029 - 0.059: 119 0.059 - 0.088: 25 0.088 - 0.117: 18 0.117 - 0.146: 7 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 23 " pdb=" N ILE A 23 " pdb=" C ILE A 23 " pdb=" CB ILE A 23 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 441 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 49 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 50 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C LEU A 160 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU A 161 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 249 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 250 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.015 5.00e-02 4.00e+02 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 393 2.18 - 2.78: 10869 2.78 - 3.39: 15468 3.39 - 3.99: 21281 3.99 - 4.60: 31835 Nonbonded interactions: 79846 Sorted by model distance: nonbonded pdb=" OD1 ASN B 21 " pdb=" H PHE B 22 " model vdw 1.575 1.850 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.578 1.850 nonbonded pdb=" HE ARG A 21 " pdb=" OD2 ASP A 39 " model vdw 1.628 1.850 nonbonded pdb=" H LYS B 41 " pdb=" O GLU B 44 " model vdw 1.656 1.850 nonbonded pdb=" OD1 ASP A 77 " pdb=" H VAL C 10 " model vdw 1.684 1.850 ... (remaining 79841 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=0.52 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: 0.020 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: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.960 Find NCS groups from input model: 0.070 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:8.350 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.028 3232 Z= 0.142 Angle : 0.446 3.633 4383 Z= 0.247 Chirality : 0.040 0.146 444 Planarity : 0.003 0.040 575 Dihedral : 12.874 82.146 1180 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.38 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.41 (0.41), residues: 376 helix: 0.82 (0.59), residues: 66 sheet: -0.63 (0.45), residues: 129 loop : -1.85 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR A 159 PHE 0.005 0.001 PHE A 208 TRP 0.007 0.001 TRP A 204 HIS 0.002 0.001 HIS A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3232 Z= 0.271 Angle : 0.498 4.103 4383 Z= 0.267 Chirality : 0.060 0.200 444 Planarity : 0.004 0.029 575 Dihedral : 12.336 81.403 1180 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.37 % Favored : 88.56 % Rotamer: Outliers : 0.60 % Allowed : 0.30 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -3.04 (0.38), residues: 376 helix: -0.67 (0.56), residues: 66 sheet: -1.44 (0.43), residues: 127 loop : -3.01 (0.37), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.012 0.001 TYR A 159 PHE 0.015 0.002 PHE B 56 TRP 0.005 0.001 TRP A 204 HIS 0.003 0.001 HIS A 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 overall best weight: 9.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3232 Z= 0.403 Angle : 0.567 4.607 4383 Z= 0.304 Chirality : 0.063 0.204 444 Planarity : 0.004 0.034 575 Dihedral : 12.882 92.008 1180 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 1.33 % Allowed : 14.36 % Favored : 84.31 % Rotamer: Outliers : 0.90 % Allowed : 3.31 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -4.03 (0.36), residues: 376 helix: -1.57 (0.53), residues: 66 sheet: -1.83 (0.43), residues: 127 loop : -3.82 (0.34), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.013 0.002 TYR A 99 PHE 0.022 0.003 PHE B 56 TRP 0.006 0.001 TRP A 204 HIS 0.005 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3232 Z= 0.331 Angle : 0.504 4.185 4383 Z= 0.269 Chirality : 0.060 0.196 444 Planarity : 0.003 0.032 575 Dihedral : 12.538 84.140 1180 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 1.06 % Allowed : 14.10 % Favored : 84.84 % Rotamer: Outliers : 1.20 % Allowed : 3.01 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -4.05 (0.36), residues: 376 helix: -1.68 (0.51), residues: 72 sheet: -1.85 (0.43), residues: 127 loop : -3.84 (0.33), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.013 0.002 TYR A 159 PHE 0.019 0.002 PHE B 56 TRP 0.005 0.001 TRP A 244 HIS 0.004 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.006 0.056 3232 Z= 0.409 Angle : 0.569 4.604 4383 Z= 0.306 Chirality : 0.063 0.201 444 Planarity : 0.004 0.035 575 Dihedral : 12.909 94.923 1180 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % Rotamer: Outliers : 1.20 % Allowed : 4.52 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -4.32 (0.35), residues: 376 helix: -2.07 (0.50), residues: 72 sheet: -1.86 (0.42), residues: 128 loop : -4.07 (0.33), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.014 0.002 TYR A 159 PHE 0.021 0.003 PHE B 56 TRP 0.006 0.001 TRP A 204 HIS 0.006 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3232 Z= 0.394 Angle : 0.545 4.455 4383 Z= 0.293 Chirality : 0.062 0.200 444 Planarity : 0.004 0.035 575 Dihedral : 12.866 92.019 1180 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 2.39 % Allowed : 14.63 % Favored : 82.98 % Rotamer: Outliers : 1.81 % Allowed : 6.02 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -4.28 (0.36), residues: 376 helix: -2.04 (0.51), residues: 72 sheet: -1.79 (0.43), residues: 128 loop : -4.08 (0.35), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.015 0.002 TYR A 159 PHE 0.020 0.002 PHE B 56 TRP 0.005 0.001 TRP A 244 HIS 0.006 0.001 HIS B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 221.57 seconds wall clock time: 4 minutes 19.01 seconds (259.01 seconds total)