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/8vi2_43246.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.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/8vi2_43246.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi2_43246.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= 0.020 sd= 0.076 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 2490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 260": "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: 4943 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4943 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 1.60, per 1000 atoms: 0.32 Number of scatterers: 4943 At special positions: 0 Unit cell: (56.6, 55.468, 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 2490 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: 2.04 Conformation dependent library (CDL) restraints added in 271.9 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.30 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: 2489 1.14 - 1.31: 356 1.31 - 1.47: 1106 1.47 - 1.64: 1056 1.64 - 1.80: 17 Bond restraints: 5024 Sorted by residual: bond pdb=" N VAL A 47 " pdb=" H VAL A 47 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N ILE A 46 " pdb=" H ILE A 46 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLY A 263 " pdb=" H GLY A 263 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N ALA A 48 " pdb=" H ALA A 48 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" N SER A 41 " pdb=" H SER A 41 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 5019 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 194 107.32 - 113.99: 5685 113.99 - 120.65: 1992 120.65 - 127.32: 1173 127.32 - 133.98: 38 Bond angle restraints: 9082 Sorted by residual: angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" C PRO A 8 " ideal model delta sigma weight residual 114.20 116.31 -2.11 1.20e+00 6.94e-01 3.10e+00 angle pdb=" CA GLU A 68 " pdb=" CB GLU A 68 " pdb=" CG GLU A 68 " ideal model delta sigma weight residual 114.10 117.03 -2.93 2.00e+00 2.50e-01 2.15e+00 angle pdb=" C ASP A 224 " pdb=" CA ASP A 224 " pdb=" CB ASP A 224 " ideal model delta sigma weight residual 114.11 110.70 3.41 2.44e+00 1.68e-01 1.96e+00 angle pdb=" CA LEU A 9 " pdb=" CB LEU A 9 " pdb=" HB2 LEU A 9 " ideal model delta sigma weight residual 109.00 104.86 4.14 3.00e+00 1.11e-01 1.91e+00 angle pdb=" CG LEU A 9 " pdb=" CB LEU A 9 " pdb=" HB2 LEU A 9 " ideal model delta sigma weight residual 108.00 104.36 3.64 3.00e+00 1.11e-01 1.47e+00 ... (remaining 9077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1621 16.33 - 32.65: 113 32.65 - 48.98: 50 48.98 - 65.30: 24 65.30 - 81.63: 2 Dihedral angle restraints: 1810 sinusoidal: 1211 harmonic: 599 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 125.69 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB LYS A 251 " pdb=" CG LYS A 251 " pdb=" CD LYS A 251 " pdb=" CE LYS A 251 " ideal model delta sinusoidal sigma weight residual 180.00 127.03 52.97 3 1.50e+01 4.44e-03 9.16e+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 -107.94 47.94 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 1807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 233 0.024 - 0.048: 97 0.048 - 0.072: 33 0.072 - 0.096: 20 0.096 - 0.120: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 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 3.17e-01 chirality pdb=" CA VAL A 223 " pdb=" N VAL A 223 " pdb=" C VAL A 223 " pdb=" CB VAL A 223 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 9 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 10 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 7 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 144 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.66e-01 pdb=" N PRO A 145 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.014 5.00e-02 4.00e+02 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 342 2.08 - 2.71: 7385 2.71 - 3.34: 15624 3.34 - 3.97: 20442 3.97 - 4.60: 30037 Nonbonded interactions: 73830 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.447 1.850 nonbonded pdb=" O SER A 261 " pdb=" H ALA A 265 " model vdw 1.487 1.850 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.518 1.850 nonbonded pdb=" O VAL A 212 " pdb=" H LEU A 216 " model vdw 1.531 1.850 nonbonded pdb=" O THR A 121 " pdb=" HG SER A 125 " model vdw 1.553 1.850 ... (remaining 73825 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: 0.020 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:5.070 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 0.019 2534 Z= 0.102 Angle : 0.423 4.250 3457 Z= 0.230 Chirality : 0.036 0.120 390 Planarity : 0.004 0.029 420 Dihedral : 11.751 81.625 856 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % 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: 0.10 (0.50), residues: 306 helix: 0.10 (0.34), residues: 239 sheet: None (None), residues: 0 loop : 0.53 (0.89), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.006 0.001 TYR A 233 PHE 0.010 0.001 PHE A 197 TRP 0.007 0.001 TRP A 231 HIS 0.001 0.000 HIS A 163 *********************** 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: 10.0000 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 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: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2534 Z= 0.156 Angle : 0.429 4.395 3457 Z= 0.218 Chirality : 0.043 0.172 390 Planarity : 0.004 0.027 420 Dihedral : 10.979 83.970 856 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % 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: 2.12 (0.50), residues: 306 helix: 1.53 (0.34), residues: 237 sheet: None (None), residues: 0 loop : 1.32 (0.85), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 243 TYR 0.006 0.001 TYR A 233 PHE 0.011 0.001 PHE A 133 TRP 0.007 0.001 TRP A 247 HIS 0.001 0.001 HIS A 187 *********************** 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: 8.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2534 Z= 0.201 Angle : 0.426 4.376 3457 Z= 0.217 Chirality : 0.043 0.155 390 Planarity : 0.004 0.032 420 Dihedral : 10.781 84.496 856 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % 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: 1.81 (0.49), residues: 306 helix: 1.31 (0.34), residues: 240 sheet: None (None), residues: 0 loop : 1.18 (0.84), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.006 0.001 TYR A 66 PHE 0.009 0.001 PHE A 133 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 220 *********************** 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: 20.0000 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 23 optimal weight: 8.9990 overall best weight: 5.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2534 Z= 0.112 Angle : 0.362 4.304 3457 Z= 0.179 Chirality : 0.040 0.158 390 Planarity : 0.004 0.029 420 Dihedral : 10.442 85.666 856 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % 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: 2.26 (0.49), residues: 306 helix: 1.59 (0.34), residues: 238 sheet: None (None), residues: 0 loop : 1.54 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.006 0.001 TYR A 66 PHE 0.009 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 276 *********************** 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: 6.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 0.0040 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2534 Z= 0.130 Angle : 0.364 4.292 3457 Z= 0.181 Chirality : 0.039 0.151 390 Planarity : 0.004 0.029 420 Dihedral : 10.199 86.321 856 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % 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: 2.27 (0.50), residues: 306 helix: 1.60 (0.35), residues: 238 sheet: None (None), residues: 0 loop : 1.53 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.005 0.001 TYR A 66 PHE 0.008 0.001 PHE A 34 TRP 0.005 0.001 TRP A 100 HIS 0.001 0.000 HIS A 220 *********************** 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: 10.0000 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2534 Z= 0.107 Angle : 0.352 4.292 3457 Z= 0.173 Chirality : 0.039 0.152 390 Planarity : 0.003 0.029 420 Dihedral : 10.025 86.797 856 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % 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: 2.40 (0.50), residues: 306 helix: 1.69 (0.35), residues: 238 sheet: None (None), residues: 0 loop : 1.57 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.006 0.001 TYR A 167 PHE 0.008 0.001 PHE A 34 TRP 0.006 0.001 TRP A 247 HIS 0.001 0.000 HIS A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 544.86 seconds wall clock time: 9 minutes 36.40 seconds (576.40 seconds total)