Starting phenix.real_space_refine on Sun May 19 16:31:30 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=True secondary_structure.enabled=False 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 { 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= 0.016 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: 1.40, per 1000 atoms: 0.28 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 293.9 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.45 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: 477 2.14 - 2.75: 8748 2.75 - 3.37: 15303 3.37 - 3.98: 20156 3.98 - 4.60: 29950 Nonbonded interactions: 74634 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 74629 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: 0.030 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: 0.040 Extract box with map and model: 0.270 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.060 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:6.130 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- 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= 0.101 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 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 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: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2534 Z= 0.154 Angle : 0.414 4.681 3457 Z= 0.203 Chirality : 0.041 0.196 390 Planarity : 0.003 0.027 420 Dihedral : 10.502 56.094 856 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.00 (0.47), residues: 306 helix: 0.18 (0.32), residues: 242 sheet: None (None), residues: 0 loop : -0.13 (0.82), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.005 0.001 TYR A 304 PHE 0.009 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.000 HIS A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2534 Z= 0.171 Angle : 0.409 4.614 3457 Z= 0.202 Chirality : 0.041 0.183 390 Planarity : 0.004 0.032 420 Dihedral : 10.267 58.544 856 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: 0.74 (0.46), residues: 306 helix: 0.78 (0.31), residues: 240 sheet: None (None), residues: 0 loop : -0.22 (0.83), residues: 66 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 0.008 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2534 Z= 0.076 Angle : 0.344 4.578 3457 Z= 0.162 Chirality : 0.038 0.151 390 Planarity : 0.003 0.029 420 Dihedral : 9.336 57.500 856 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: 1.79 (0.47), residues: 306 helix: 1.57 (0.33), residues: 242 sheet: None (None), residues: 0 loop : -0.09 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.006 0.001 TYR A 304 PHE 0.006 0.001 PHE A 34 TRP 0.005 0.001 TRP A 247 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.9184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2074 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= 0.082 Angle : 0.346 4.537 3457 Z= 0.163 Chirality : 0.038 0.155 390 Planarity : 0.003 0.026 420 Dihedral : 8.974 55.830 856 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: 2.19 (0.49), residues: 306 helix: 1.82 (0.33), residues: 242 sheet: None (None), residues: 0 loop : 0.16 (0.83), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.005 0.001 TYR A 304 PHE 0.007 0.001 PHE A 34 TRP 0.004 0.001 TRP A 100 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2534 Z= 0.219 Angle : 0.437 4.687 3457 Z= 0.217 Chirality : 0.043 0.200 390 Planarity : 0.004 0.031 420 Dihedral : 9.785 54.496 856 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: 1.30 (0.49), residues: 306 helix: 1.17 (0.34), residues: 242 sheet: None (None), residues: 0 loop : -0.04 (0.83), residues: 64 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 133 TRP 0.008 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: 561.63 seconds wall clock time: 9 minutes 56.12 seconds (596.12 seconds total)