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/7pcq_13325.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.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=3.62 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" } resolution = 3.62 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= 0.024 sd= 0.035 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 6 5.16 5 C 1409 2.51 5 N 382 2.21 5 O 395 1.98 5 H 2189 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: 4381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2145 Classifications: {'peptide': 141} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2236 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 1.09, per 1000 atoms: 0.25 Number of scatterers: 4381 At special positions: 0 Unit cell: (58.68, 61.94, 68.46, 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 6 16.00 O 395 8.00 N 382 7.00 C 1409 6.00 H 2189 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: 1.36 Conformation dependent library (CDL) restraints added in 255.4 milliseconds 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 1.56 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: 2186 1.14 - 1.31: 360 1.31 - 1.48: 910 1.48 - 1.65: 974 1.65 - 1.81: 9 Bond restraints: 4439 Sorted by residual: bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N ALA B 62 " pdb=" H ALA B 62 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" N SER A 84 " pdb=" H SER A 84 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N VAL A 93 " pdb=" H VAL A 93 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N TYR B 35 " pdb=" H TYR B 35 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 4434 not shown) Histogram of bond angle deviations from ideal: 100.96 - 107.55: 246 107.55 - 114.14: 5234 114.14 - 120.73: 1488 120.73 - 127.32: 1044 127.32 - 133.91: 38 Bond angle restraints: 8050 Sorted by residual: angle pdb=" N GLY A 18 " pdb=" CA GLY A 18 " pdb=" C GLY A 18 " ideal model delta sigma weight residual 110.77 115.07 -4.30 1.93e+00 2.68e-01 4.97e+00 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 110.70 112.49 -1.79 1.22e+00 6.72e-01 2.15e+00 angle pdb=" CA PRO B 124 " pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 117.93 119.33 -1.40 1.20e+00 6.94e-01 1.37e+00 angle pdb=" C THR A 118 " pdb=" N PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 125.00 129.46 -4.46 4.10e+00 5.95e-02 1.18e+00 angle pdb=" C PRO B 124 " pdb=" N PRO B 125 " pdb=" CD PRO B 125 " ideal model delta sigma weight residual 125.00 129.38 -4.38 4.10e+00 5.95e-02 1.14e+00 ... (remaining 8045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 1398 15.73 - 31.47: 95 31.47 - 47.20: 40 47.20 - 62.94: 31 62.94 - 78.67: 1 Dihedral angle restraints: 1565 sinusoidal: 1097 harmonic: 468 Sorted by residual: dihedral pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG B 40 " pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N PHE A 46 " pdb=" CA PHE A 46 " pdb=" CB PHE A 46 " pdb=" CG PHE A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -102.13 42.13 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 1562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 222 0.022 - 0.044: 77 0.044 - 0.066: 19 0.066 - 0.088: 26 0.088 - 0.109: 6 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA PRO B 36 " pdb=" N PRO B 36 " pdb=" C PRO B 36 " pdb=" CB PRO B 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" C PRO A 77 " pdb=" CB PRO A 77 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.10e-01 ... (remaining 347 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 124 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 35 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO B 36 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 3 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.27e-01 pdb=" N PRO A 4 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " -0.012 5.00e-02 4.00e+02 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 576 2.24 - 2.83: 9243 2.83 - 3.42: 12542 3.42 - 4.01: 16136 4.01 - 4.60: 24668 Nonbonded interactions: 63165 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" H HIS A 122 " model vdw 1.647 1.850 nonbonded pdb=" HE1 TRP A 14 " pdb=" OG1 THR A 67 " model vdw 1.651 1.850 nonbonded pdb=" O THR B 4 " pdb=" H LYS B 8 " model vdw 1.670 1.850 nonbonded pdb=" OE1 GLU A 27 " pdb=" HE2 HIS A 112 " model vdw 1.779 1.850 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.787 2.100 ... (remaining 63160 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: 0.030 Extract box with map and model: 0.210 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 7.920 Find NCS groups from input model: 0.040 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:4.470 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.042 2250 Z= 0.110 Angle : 0.442 4.460 3061 Z= 0.241 Chirality : 0.032 0.109 350 Planarity : 0.003 0.028 391 Dihedral : 10.870 78.670 784 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 2.20 (0.46), residues: 283 helix: 1.71 (0.32), residues: 220 sheet: None (None), residues: 0 loop : 0.79 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.003 0.001 TYR B 145 PHE 0.006 0.001 PHE A 46 TRP 0.004 0.001 TRP A 14 HIS 0.002 0.001 HIS B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2250 Z= 0.145 Angle : 0.457 4.604 3061 Z= 0.239 Chirality : 0.037 0.125 350 Planarity : 0.004 0.026 391 Dihedral : 9.144 67.372 784 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.48), residues: 283 helix: 2.77 (0.33), residues: 221 sheet: None (None), residues: 0 loop : 1.40 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 31 TYR 0.004 0.001 TYR A 42 PHE 0.006 0.001 PHE B 71 TRP 0.002 0.000 TRP B 15 HIS 0.002 0.000 HIS B 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2250 Z= 0.124 Angle : 0.401 4.701 3061 Z= 0.201 Chirality : 0.036 0.142 350 Planarity : 0.003 0.027 391 Dihedral : 7.979 50.783 784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.48), residues: 283 helix: 2.79 (0.32), residues: 221 sheet: None (None), residues: 0 loop : 1.69 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.002 0.001 TYR A 24 PHE 0.005 0.001 PHE A 46 TRP 0.004 0.001 TRP B 37 HIS 0.002 0.000 HIS A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 0.0670 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 overall best weight: 8.8130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2250 Z= 0.128 Angle : 0.385 4.530 3061 Z= 0.196 Chirality : 0.035 0.119 350 Planarity : 0.003 0.027 391 Dihedral : 7.358 41.994 784 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.43 % Allowed : 1.30 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.47), residues: 283 helix: 2.73 (0.32), residues: 218 sheet: None (None), residues: 0 loop : 1.59 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.002 0.000 TYR B 145 PHE 0.004 0.001 PHE B 45 TRP 0.003 0.001 TRP B 37 HIS 0.002 0.000 HIS B 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2250 Z= 0.164 Angle : 0.440 4.617 3061 Z= 0.228 Chirality : 0.036 0.121 350 Planarity : 0.003 0.024 391 Dihedral : 7.292 37.602 784 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.87 % Allowed : 1.73 % Favored : 97.40 % 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: 2.88 (0.47), residues: 283 helix: 2.10 (0.32), residues: 217 sheet: None (None), residues: 0 loop : 1.49 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.004 0.001 TYR B 130 PHE 0.005 0.001 PHE A 117 TRP 0.004 0.001 TRP A 14 HIS 0.003 0.001 HIS B 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2250 Z= 0.188 Angle : 0.440 4.662 3061 Z= 0.233 Chirality : 0.035 0.116 350 Planarity : 0.003 0.024 391 Dihedral : 7.197 39.219 784 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.87 % Allowed : 1.73 % Favored : 97.40 % 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 (0.47), residues: 283 helix: 1.66 (0.32), residues: 211 sheet: None (None), residues: 0 loop : 1.33 (0.82), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.004 0.001 TYR B 130 PHE 0.005 0.001 PHE A 117 TRP 0.004 0.001 TRP B 37 HIS 0.002 0.001 HIS B 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 517.91 seconds wall clock time: 9 minutes 11.20 seconds (551.20 seconds total)