Starting phenix.real_space_refine on Sun May 19 16:31:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.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=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5xb1_6714.map" } resolution = 3.0 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= 0.049 sd= 0.288 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 7 5.16 5 C 802 2.51 5 N 228 2.21 5 O 247 1.98 5 H 1238 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: 2522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2522 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Time building chain proxies: 0.58, per 1000 atoms: 0.23 Number of scatterers: 2522 At special positions: 0 Unit cell: (65.6731, 58.6866, 65.6731, 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 7 16.00 O 247 8.00 N 228 7.00 C 802 6.00 H 1238 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: 0.52 Conformation dependent library (CDL) restraints added in 106.3 milliseconds 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 0.60 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: 1235 1.14 - 1.31: 230 1.31 - 1.48: 512 1.48 - 1.64: 559 1.64 - 1.81: 11 Bond restraints: 2547 Sorted by residual: bond pdb=" ND2 ASN A 110 " pdb="HD22 ASN A 110 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N HIS A 129 " pdb=" H HIS A 129 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" NH2 ARG A 23 " pdb="HH22 ARG A 23 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N TYR A 138 " pdb=" H TYR A 138 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" N ASN A 140 " pdb=" H ASN A 140 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.85: 30 106.85 - 113.61: 2943 113.61 - 120.37: 869 120.37 - 127.13: 726 127.13 - 133.89: 13 Bond angle restraints: 4581 Sorted by residual: angle pdb=" C VAL A 9 " pdb=" CA VAL A 9 " pdb=" CB VAL A 9 " ideal model delta sigma weight residual 111.85 109.82 2.03 1.27e+00 6.20e-01 2.56e+00 angle pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta sigma weight residual 122.53 119.70 2.83 1.92e+00 2.71e-01 2.18e+00 angle pdb=" N TYR A 138 " pdb=" CA TYR A 138 " pdb=" C TYR A 138 " ideal model delta sigma weight residual 113.12 114.78 -1.66 1.25e+00 6.40e-01 1.76e+00 angle pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 117.60 119.41 -1.81 1.39e+00 5.18e-01 1.69e+00 angle pdb=" C THR A 136 " pdb=" N HIS A 137 " pdb=" CA HIS A 137 " ideal model delta sigma weight residual 122.60 120.23 2.37 1.88e+00 2.83e-01 1.59e+00 ... (remaining 4576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 837 16.71 - 33.41: 34 33.41 - 50.12: 15 50.12 - 66.83: 2 66.83 - 83.53: 4 Dihedral angle restraints: 892 sinusoidal: 640 harmonic: 252 Sorted by residual: dihedral pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 151 " pdb=" C ASP A 151 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " ideal model delta harmonic sigma weight residual 180.00 164.89 15.11 0 5.00e+00 4.00e-02 9.14e+00 dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual 180.00 167.53 12.47 0 5.00e+00 4.00e-02 6.22e+00 ... (remaining 889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 121 0.024 - 0.049: 44 0.049 - 0.073: 11 0.073 - 0.097: 6 0.097 - 0.121: 3 Chirality restraints: 185 Sorted by residual: chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 182 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 127 " 0.012 5.00e-02 4.00e+02 1.88e-02 5.65e-01 pdb=" N PRO A 128 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 88 " -0.012 5.00e-02 4.00e+02 1.76e-02 4.94e-01 pdb=" N PRO A 89 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " -0.003 2.00e-02 2.50e+03 6.39e-03 4.08e-01 pdb=" C GLU A 28 " 0.011 2.00e-02 2.50e+03 pdb=" O GLU A 28 " -0.004 2.00e-02 2.50e+03 pdb=" N LEU A 29 " -0.004 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 396 2.32 - 2.89: 5445 2.89 - 3.46: 6421 3.46 - 4.03: 8126 4.03 - 4.60: 12102 Nonbonded interactions: 32490 Sorted by model distance: nonbonded pdb=" OD1 ASP A 92 " pdb=" H ASP A 93 " model vdw 1.744 1.850 nonbonded pdb=" O ASP A 132 " pdb=" HG1 THR A 136 " model vdw 1.765 1.850 nonbonded pdb=" O SER A 32 " pdb=" HG SER A 60 " model vdw 1.778 1.850 nonbonded pdb=" H GLN A 15 " pdb=" HG2 GLN A 15 " model vdw 1.820 2.270 nonbonded pdb=" HH TYR A 35 " pdb=" OE2 GLU A 108 " model vdw 1.843 1.850 ... (remaining 32485 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=0.51 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.970 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:2.520 Internal consistency checks: 0.000 Total: 7.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.003 0.017 1309 Z= 0.175 Angle : 0.455 3.044 1762 Z= 0.276 Chirality : 0.032 0.121 185 Planarity : 0.003 0.019 233 Dihedral : 11.226 83.533 496 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.23 (0.63), residues: 153 helix: 0.88 (0.44), residues: 117 sheet: None (None), residues: 0 loop : -2.19 (0.91), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.010 0.001 TYR A 33 PHE 0.005 0.001 PHE A 133 TRP 0.005 0.001 TRP A 94 HIS 0.002 0.001 HIS A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1309 Z= 0.121 Angle : 0.401 3.260 1762 Z= 0.217 Chirality : 0.039 0.129 185 Planarity : 0.003 0.016 233 Dihedral : 11.705 80.721 496 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.50 (0.68), residues: 153 helix: 1.63 (0.47), residues: 123 sheet: None (None), residues: 0 loop : -1.68 (1.05), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 80 TYR 0.010 0.002 TYR A 40 PHE 0.004 0.001 PHE A 52 TRP 0.008 0.002 TRP A 94 HIS 0.003 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1309 Z= 0.086 Angle : 0.316 3.161 1762 Z= 0.174 Chirality : 0.036 0.130 185 Planarity : 0.002 0.018 233 Dihedral : 11.033 75.839 496 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.72 (0.69), residues: 153 helix: 1.75 (0.47), residues: 123 sheet: None (None), residues: 0 loop : -1.41 (1.09), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.010 0.002 TYR A 33 PHE 0.005 0.001 PHE A 56 TRP 0.006 0.002 TRP A 94 HIS 0.003 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1309 Z= 0.073 Angle : 0.310 3.207 1762 Z= 0.170 Chirality : 0.035 0.131 185 Planarity : 0.002 0.021 233 Dihedral : 10.887 73.213 496 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.67), residues: 153 helix: 1.74 (0.47), residues: 123 sheet: None (None), residues: 0 loop : -1.03 (1.04), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.009 0.002 TYR A 33 PHE 0.004 0.001 PHE A 56 TRP 0.006 0.002 TRP A 94 HIS 0.003 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1309 Z= 0.087 Angle : 0.327 3.125 1762 Z= 0.179 Chirality : 0.036 0.131 185 Planarity : 0.003 0.022 233 Dihedral : 11.073 71.171 496 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.54 (0.66), residues: 153 helix: 1.45 (0.46), residues: 123 sheet: None (None), residues: 0 loop : -0.61 (1.11), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.010 0.002 TYR A 33 PHE 0.004 0.001 PHE A 56 TRP 0.006 0.002 TRP A 94 HIS 0.003 0.001 HIS A 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1309 Z= 0.130 Angle : 0.387 3.191 1762 Z= 0.213 Chirality : 0.038 0.139 185 Planarity : 0.003 0.023 233 Dihedral : 12.063 71.399 496 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.47 (0.64), residues: 153 helix: 0.67 (0.44), residues: 122 sheet: None (None), residues: 0 loop : -0.75 (1.09), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.012 0.002 TYR A 40 PHE 0.006 0.001 PHE A 42 TRP 0.007 0.002 TRP A 94 HIS 0.004 0.001 HIS A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 441.48 seconds wall clock time: 7 minutes 48.49 seconds (468.49 seconds total)