Starting phenix.real_space_refine on Sun May 19 16:31:30 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.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=3.19 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.pdb" } resolution = 3.19 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= 0.005 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 856 atoms to isotropic. 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 45 5.16 5 C 4610 2.51 5 N 1223 2.21 5 O 1399 1.98 5 H 7071 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 14348 Number of models: 1 Model: "" Number of chains: 5 Chain: "0" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3851 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "1" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3592 Classifications: {'peptide': 237} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "2" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 864 Inner-chain residues flagged as termini: ['pdbres="HIS 2 13 "', 'pdbres="ILE 2 25 "'] Classifications: {'peptide': 56} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 1 Chain: "3" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1849 Classifications: {'peptide': 118} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "4" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4192 Classifications: {'peptide': 268} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 248} Time building chain proxies: 3.59, per 1000 atoms: 0.25 Number of scatterers: 14348 At special positions: 0 Unit cell: (128.52, 97.2, 92.88, 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 45 16.00 O 1399 8.00 N 1223 7.00 C 4610 6.00 H 7071 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 101 " distance=2.04 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: 5.23 Conformation dependent library (CDL) restraints added in 637.5 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 5.90 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: 7052 1.15 - 1.31: 1218 1.31 - 1.48: 3095 1.48 - 1.65: 3102 1.65 - 1.81: 69 Bond restraints: 14536 Sorted by residual: bond pdb=" N TRP 4 159 " pdb=" H TRP 4 159 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N SER 3 85 " pdb=" H SER 3 85 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ILE 4 207 " pdb=" H ILE 4 207 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N HIS 0 118 " pdb=" H HIS 0 118 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N ASN 0 165 " pdb=" H ASN 0 165 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 14531 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 370 106.98 - 113.74: 17170 113.74 - 120.50: 4438 120.50 - 127.26: 4122 127.26 - 134.02: 106 Bond angle restraints: 26206 Sorted by residual: angle pdb=" CA TRP 4 159 " pdb=" C TRP 4 159 " pdb=" N GLN 4 160 " ideal model delta sigma weight residual 116.84 121.27 -4.43 1.71e+00 3.42e-01 6.73e+00 angle pdb=" N GLY 0 90 " pdb=" CA GLY 0 90 " pdb=" C GLY 0 90 " ideal model delta sigma weight residual 112.45 117.81 -5.36 2.10e+00 2.27e-01 6.52e+00 angle pdb=" C ILE 3 52 " pdb=" N ILE 3 53 " pdb=" CA ILE 3 53 " ideal model delta sigma weight residual 122.71 119.20 3.51 1.44e+00 4.82e-01 5.95e+00 angle pdb=" N THR 4 276 " pdb=" CA THR 4 276 " pdb=" C THR 4 276 " ideal model delta sigma weight residual 113.56 110.47 3.09 1.39e+00 5.18e-01 4.94e+00 angle pdb=" C LEU 1 132 " pdb=" N ALA 1 133 " pdb=" CA ALA 1 133 " ideal model delta sigma weight residual 121.85 118.10 3.75 1.77e+00 3.19e-01 4.50e+00 ... (remaining 26201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4601 15.22 - 30.44: 413 30.44 - 45.67: 148 45.67 - 60.89: 79 60.89 - 76.11: 3 Dihedral angle restraints: 5244 sinusoidal: 3753 harmonic: 1491 Sorted by residual: dihedral pdb=" CA TYR 0 106 " pdb=" C TYR 0 106 " pdb=" N THR 0 107 " pdb=" CA THR 0 107 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" N ASN 4 55 " pdb=" CA ASN 4 55 " pdb=" CB ASN 4 55 " pdb=" CG ASN 4 55 " ideal model delta sinusoidal sigma weight residual -180.00 -120.58 -59.42 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA MET 1 211 " pdb=" CB MET 1 211 " pdb=" CG MET 1 211 " pdb=" SD MET 1 211 " ideal model delta sinusoidal sigma weight residual -60.00 -118.28 58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 722 0.034 - 0.067: 282 0.067 - 0.101: 65 0.101 - 0.134: 55 0.134 - 0.168: 7 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA VAL 0 124 " pdb=" N VAL 0 124 " pdb=" C VAL 0 124 " pdb=" CB VAL 0 124 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE 0 243 " pdb=" N ILE 0 243 " pdb=" C ILE 0 243 " pdb=" CB ILE 0 243 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE 1 190 " pdb=" N ILE 1 190 " pdb=" C ILE 1 190 " pdb=" CB ILE 1 190 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1128 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 0 127 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO 0 128 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO 0 128 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO 0 128 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU 2 55 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO 2 56 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO 2 56 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 56 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 0 75 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO 0 76 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO 0 76 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 0 76 " 0.021 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1003 2.17 - 2.78: 25160 2.78 - 3.38: 36167 3.38 - 3.99: 49707 3.99 - 4.60: 71777 Nonbonded interactions: 183814 Sorted by model distance: nonbonded pdb=" O THR 1 98 " pdb=" H GLU 1 102 " model vdw 1.560 1.850 nonbonded pdb=" O GLU 0 27 " pdb="HD22 ASN 0 198 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP 0 44 " pdb="HH21 ARG 4 51 " model vdw 1.616 1.850 nonbonded pdb=" HG1 THR 3 17 " pdb=" O THR 3 89 " model vdw 1.618 1.850 nonbonded pdb=" HG1 THR 0 136 " pdb=" O ASN 0 165 " model vdw 1.646 1.850 ... (remaining 183809 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.150 Extract box with map and model: 0.760 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.690 Find NCS groups from input model: 0.200 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:17.800 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 0.031 7465 Z= 0.138 Angle : 0.507 5.361 10184 Z= 0.277 Chirality : 0.044 0.168 1131 Planarity : 0.004 0.038 1323 Dihedral : 10.882 75.509 2691 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.10 % Favored : 94.47 % Rotamer: Outliers : 2.47 % Allowed : 5.07 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.69 (0.24), residues: 922 helix: -2.98 (0.45), residues: 67 sheet: 0.18 (0.30), residues: 270 loop : -1.60 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 102 TYR 0.015 0.001 TYR 0 173 PHE 0.008 0.001 PHE 1 120 TRP 0.010 0.001 TRP 0 79 HIS 0.003 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7465 Z= 0.157 Angle : 0.462 4.461 10184 Z= 0.228 Chirality : 0.056 0.159 1131 Planarity : 0.004 0.034 1323 Dihedral : 10.519 67.948 2691 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 2.10 % Allowed : 4.57 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.25 (0.25), residues: 922 helix: -2.08 (0.55), residues: 67 sheet: 0.32 (0.30), residues: 276 loop : -1.31 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 102 TYR 0.011 0.001 TYR 0 173 PHE 0.007 0.001 PHE 4 67 TRP 0.006 0.001 TRP 0 79 HIS 0.004 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7465 Z= 0.217 Angle : 0.486 4.761 10184 Z= 0.243 Chirality : 0.060 0.169 1131 Planarity : 0.004 0.038 1323 Dihedral : 10.234 58.530 2691 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.90 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 4.33 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.30 (0.25), residues: 922 helix: -2.17 (0.53), residues: 68 sheet: 0.23 (0.31), residues: 264 loop : -1.27 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 102 TYR 0.010 0.001 TYR 0 173 PHE 0.010 0.001 PHE 4 67 TRP 0.009 0.001 TRP 0 79 HIS 0.004 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 overall best weight: 3.9044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7465 Z= 0.098 Angle : 0.399 4.585 10184 Z= 0.192 Chirality : 0.055 0.152 1131 Planarity : 0.003 0.032 1323 Dihedral : 9.655 59.526 2691 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % Rotamer: Outliers : 1.61 % Allowed : 4.08 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.14 (0.25), residues: 922 helix: -1.85 (0.57), residues: 67 sheet: 0.27 (0.31), residues: 270 loop : -1.15 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 248 TYR 0.008 0.001 TYR 0 173 PHE 0.007 0.001 PHE 4 76 TRP 0.007 0.001 TRP 0 79 HIS 0.002 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.1980 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 40.0000 chunk 56 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7465 Z= 0.139 Angle : 0.416 4.740 10184 Z= 0.202 Chirality : 0.057 0.158 1131 Planarity : 0.004 0.035 1323 Dihedral : 9.379 56.026 2691 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 1.36 % Allowed : 3.58 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.11 (0.26), residues: 922 helix: -1.79 (0.59), residues: 67 sheet: 0.40 (0.31), residues: 272 loop : -1.21 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 102 TYR 0.009 0.001 TYR 0 173 PHE 0.008 0.001 PHE 4 67 TRP 0.008 0.001 TRP 0 79 HIS 0.003 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7465 Z= 0.163 Angle : 0.429 4.739 10184 Z= 0.211 Chirality : 0.057 0.160 1131 Planarity : 0.004 0.035 1323 Dihedral : 9.423 53.183 2691 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.24 % Allowed : 3.96 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.20 (0.26), residues: 922 helix: -1.86 (0.60), residues: 67 sheet: 0.25 (0.31), residues: 273 loop : -1.22 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 248 TYR 0.009 0.001 TYR 0 173 PHE 0.008 0.001 PHE 4 67 TRP 0.007 0.001 TRP 0 79 HIS 0.003 0.001 HIS 4 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 629.07 seconds wall clock time: 11 minutes 20.88 seconds (680.88 seconds total)