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/6xmx_22265.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.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=3.7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.map" } resolution = 3.7 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= 0.004 sd= 0.009 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 11 5.16 5 C 618 2.51 5 N 170 2.21 5 O 177 1.98 5 H 1000 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: 1976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1976 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Time building chain proxies: 0.92, per 1000 atoms: 0.47 Number of scatterers: 1976 At special positions: 0 Unit cell: (58.575, 56.1, 56.925, 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 11 16.00 O 177 8.00 N 170 7.00 C 618 6.00 H 1000 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: 0.62 Conformation dependent library (CDL) restraints added in 105.2 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 995 1.15 - 1.31: 163 1.31 - 1.48: 385 1.48 - 1.65: 430 1.65 - 1.81: 17 Bond restraints: 1990 Sorted by residual: bond pdb=" N PHE A 83 " pdb=" H PHE A 83 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N LEU A 20 " pdb=" H LEU A 20 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" N ASP A 29 " pdb=" H ASP A 29 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" NH2 ARG A 44 " pdb="HH22 ARG A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" N ILE A 30 " pdb=" H ILE A 30 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 1985 not shown) Histogram of bond angle deviations from ideal: 100.64 - 106.76: 20 106.76 - 112.88: 2339 112.88 - 119.00: 393 119.00 - 125.11: 796 125.11 - 131.23: 42 Bond angle restraints: 3590 Sorted by residual: angle pdb=" C ASP A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 122.71 120.62 2.09 1.44e+00 4.82e-01 2.10e+00 angle pdb=" N THR A 62 " pdb=" CA THR A 62 " pdb=" C THR A 62 " ideal model delta sigma weight residual 112.90 111.01 1.89 1.31e+00 5.83e-01 2.09e+00 angle pdb=" N LEU A 31 " pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " ideal model delta sigma weight residual 112.78 110.84 1.94 1.53e+00 4.27e-01 1.61e+00 angle pdb=" C SER A 93 " pdb=" CA SER A 93 " pdb=" CB SER A 93 " ideal model delta sigma weight residual 110.65 108.27 2.38 1.95e+00 2.63e-01 1.49e+00 angle pdb=" C PHE A 124 " pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 121.09 119.22 1.87 1.65e+00 3.67e-01 1.29e+00 ... (remaining 3585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 614 15.72 - 31.43: 51 31.43 - 47.15: 18 47.15 - 62.86: 6 62.86 - 78.58: 2 Dihedral angle restraints: 691 sinusoidal: 510 harmonic: 181 Sorted by residual: dihedral pdb=" N GLU A 81 " pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sinusoidal sigma weight residual 180.00 126.47 53.53 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA ARG A 26 " pdb=" CB ARG A 26 " pdb=" CG ARG A 26 " pdb=" CD ARG A 26 " ideal model delta sinusoidal sigma weight residual -60.00 -104.56 44.56 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG A 44 " pdb=" CB ARG A 44 " pdb=" CG ARG A 44 " pdb=" CD ARG A 44 " ideal model delta sinusoidal sigma weight residual -180.00 -136.67 -43.33 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 99 0.026 - 0.052: 33 0.052 - 0.078: 17 0.078 - 0.103: 3 0.103 - 0.129: 8 Chirality restraints: 160 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 157 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 81 " 0.003 2.00e-02 2.50e+03 5.88e-03 3.46e-01 pdb=" C GLU A 81 " -0.010 2.00e-02 2.50e+03 pdb=" O GLU A 81 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY A 82 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 81 " 0.003 2.00e-02 2.50e+03 5.27e-03 2.78e-01 pdb=" N GLY A 82 " -0.009 2.00e-02 2.50e+03 pdb=" CA GLY A 82 " 0.002 2.00e-02 2.50e+03 pdb=" H GLY A 82 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.008 5.00e-02 4.00e+02 1.28e-02 2.62e-01 pdb=" N PRO A 80 " -0.022 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.006 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.007 5.00e-02 4.00e+02 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 143 2.14 - 2.75: 3496 2.75 - 3.37: 5504 3.37 - 3.98: 7155 3.98 - 4.60: 10363 Nonbonded interactions: 26661 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.521 1.850 nonbonded pdb=" O PHE A 89 " pdb=" H SER A 93 " model vdw 1.525 1.850 nonbonded pdb=" HZ3 LYS A 47 " pdb=" O CYS A 67 " model vdw 1.596 1.850 nonbonded pdb=" O THR A 92 " pdb=" HG SER A 93 " model vdw 1.604 1.850 nonbonded pdb=" O ASP A 88 " pdb=" HG1 THR A 92 " model vdw 1.622 1.850 ... (remaining 26656 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=0.49 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.320 Find NCS groups from input model: 0.020 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:1.880 Internal consistency checks: 0.000 Total: 7.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 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 0.012 990 Z= 0.102 Angle : 0.429 3.615 1336 Z= 0.251 Chirality : 0.040 0.129 160 Planarity : 0.002 0.013 169 Dihedral : 13.694 78.578 370 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.89 % Allowed : 0.00 % Favored : 99.11 % 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: 0.14 (0.70), residues: 120 helix: 0.52 (0.54), residues: 73 sheet: None (None), residues: 0 loop : -0.42 (0.90), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.002 0.001 TYR A 58 PHE 0.004 0.001 PHE A 43 HIS 0.001 0.001 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 990 Z= 0.138 Angle : 0.473 3.301 1336 Z= 0.258 Chirality : 0.051 0.141 160 Planarity : 0.004 0.030 169 Dihedral : 11.405 70.892 370 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 1.79 % Favored : 97.32 % 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: 0.55 (0.74), residues: 120 helix: 0.66 (0.57), residues: 72 sheet: None (None), residues: 0 loop : 0.10 (0.95), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.012 0.002 TYR A 91 PHE 0.003 0.001 PHE A 124 HIS 0.005 0.002 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 990 Z= 0.161 Angle : 0.450 3.715 1336 Z= 0.250 Chirality : 0.054 0.151 160 Planarity : 0.004 0.026 169 Dihedral : 10.942 54.819 370 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.79 % Allowed : 2.68 % Favored : 95.54 % 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: -1.01 (0.70), residues: 120 helix: -0.66 (0.55), residues: 75 sheet: None (None), residues: 0 loop : -0.40 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.012 0.002 TYR A 91 PHE 0.006 0.001 PHE A 61 HIS 0.005 0.002 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 990 Z= 0.111 Angle : 0.399 3.561 1336 Z= 0.226 Chirality : 0.051 0.153 160 Planarity : 0.004 0.036 169 Dihedral : 10.431 51.578 370 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 1.79 % Favored : 96.43 % 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: -0.77 (0.73), residues: 120 helix: -0.67 (0.57), residues: 72 sheet: None (None), residues: 0 loop : 0.05 (0.90), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.011 0.002 TYR A 91 PHE 0.005 0.001 PHE A 83 HIS 0.004 0.002 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 990 Z= 0.148 Angle : 0.461 3.697 1336 Z= 0.260 Chirality : 0.053 0.145 160 Planarity : 0.004 0.031 169 Dihedral : 10.566 50.491 370 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.79 % Allowed : 2.68 % Favored : 95.54 % 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: -1.49 (0.73), residues: 120 helix: -1.24 (0.56), residues: 72 sheet: None (None), residues: 0 loop : -0.28 (0.91), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 94 TYR 0.011 0.002 TYR A 91 PHE 0.008 0.001 PHE A 83 HIS 0.005 0.002 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 990 Z= 0.116 Angle : 0.406 3.513 1336 Z= 0.228 Chirality : 0.050 0.149 160 Planarity : 0.004 0.033 169 Dihedral : 10.207 45.172 370 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: -1.68 (0.71), residues: 120 helix: -1.50 (0.58), residues: 67 sheet: None (None), residues: 0 loop : -0.32 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.011 0.002 TYR A 91 PHE 0.004 0.001 PHE A 89 HIS 0.004 0.001 HIS A 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 465.05 seconds wall clock time: 8 minutes 13.84 seconds (493.84 seconds total)