Starting phenix.real_space_refine on Sun May 19 16:31:06 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=False secondary_structure.enabled=False resolution=3.62 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 ramachandran_plot_restraints { enabled = False } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 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: 0.91, per 1000 atoms: 0.21 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: 1.05 Conformation dependent library (CDL) restraints added in 140.8 milliseconds Time building geometry restraints manager: 1.20 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: 0.040 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.030 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:3.540 Internal consistency checks: 0.000 Total: 8.420 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1656 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= 0.090 Angle : 0.401 4.818 3061 Z= 0.188 Chirality : 0.035 0.123 350 Planarity : 0.003 0.021 391 Dihedral : 9.247 68.615 784 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -4.89 (0.37), residues: 283 helix: -3.63 (0.21), residues: 220 sheet: None (None), residues: 0 loop : -0.44 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 31 TYR 0.003 0.001 TYR B 130 PHE 0.005 0.001 PHE B 71 TRP 0.003 0.001 TRP A 14 HIS 0.002 0.000 HIS B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 overall best weight: 21.1998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2250 Z= 0.293 Angle : 0.627 5.518 3061 Z= 0.340 Chirality : 0.042 0.150 350 Planarity : 0.004 0.035 391 Dihedral : 9.664 49.997 784 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 31.94 Ramachandran Plot: Outliers : 8.13 % Allowed : 34.28 % Favored : 57.60 % Rotamer: Outliers : 2.16 % Allowed : 6.93 % Favored : 90.91 % 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: -8.06 (0.23), residues: 283 helix: -5.31 (0.08), residues: 210 sheet: None (None), residues: 0 loop : -4.43 (0.58), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.005 0.001 TYR A 140 PHE 0.009 0.001 PHE B 41 TRP 0.005 0.001 TRP B 15 HIS 0.004 0.001 HIS B 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- 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: 30.0000 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2250 Z= 0.222 Angle : 0.496 5.090 3061 Z= 0.256 Chirality : 0.037 0.123 350 Planarity : 0.003 0.025 391 Dihedral : 8.941 41.835 784 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 1.77 % Allowed : 15.90 % Favored : 82.33 % Rotamer: Outliers : 2.16 % Allowed : 5.19 % Favored : 92.64 % 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: -7.52 (0.26), residues: 283 helix: -5.16 (0.09), residues: 210 sheet: None (None), residues: 0 loop : -3.35 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.004 0.001 TYR A 140 PHE 0.007 0.001 PHE A 117 TRP 0.004 0.001 TRP A 14 HIS 0.005 0.001 HIS B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2250 Z= 0.252 Angle : 0.524 5.203 3061 Z= 0.282 Chirality : 0.039 0.143 350 Planarity : 0.003 0.028 391 Dihedral : 9.526 48.957 784 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 3.89 % Allowed : 29.33 % Favored : 66.78 % Rotamer: Outliers : 5.19 % Allowed : 6.49 % Favored : 88.31 % 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: -7.95 (0.24), residues: 283 helix: -5.41 (0.07), residues: 201 sheet: None (None), residues: 0 loop : -4.09 (0.53), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 92 TYR 0.006 0.001 TYR B 130 PHE 0.006 0.001 PHE B 41 TRP 0.005 0.001 TRP A 14 HIS 0.005 0.001 HIS B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 23 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2250 Z= 0.227 Angle : 0.490 5.104 3061 Z= 0.258 Chirality : 0.036 0.130 350 Planarity : 0.003 0.029 391 Dihedral : 9.484 52.064 784 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 3.53 % Allowed : 20.14 % Favored : 76.33 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % 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: -7.45 (0.28), residues: 283 helix: -5.24 (0.09), residues: 205 sheet: None (None), residues: 0 loop : -3.12 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 92 TYR 0.006 0.001 TYR B 130 PHE 0.005 0.001 PHE A 36 TRP 0.005 0.001 TRP B 37 HIS 0.005 0.001 HIS B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 163.98 seconds wall clock time: 3 minutes 19.18 seconds (199.18 seconds total)