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/6y9x_10740.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.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=4.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.map" } resolution = 4.4 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= 0.003 sd= 0.006 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 26 5.16 5 C 2162 2.51 5 N 598 2.21 5 O 649 1.98 5 H 3432 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: 6867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2265 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3432 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "N" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1170 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 1.94, per 1000 atoms: 0.28 Number of scatterers: 6867 At special positions: 0 Unit cell: (95.4, 125.08, 85.86, 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 26 16.00 O 649 8.00 N 598 7.00 C 2162 6.00 H 3432 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " 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: 2.65 Conformation dependent library (CDL) restraints added in 362.2 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.97 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: 3432 1.15 - 1.32: 591 1.32 - 1.49: 1346 1.49 - 1.65: 1525 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" N ILE B 37 " pdb=" H ILE B 37 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" N GLU B 28 " pdb=" H GLU B 28 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N PHE B 32 " pdb=" H PHE B 32 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N ALA B 47 " pdb=" H ALA B 47 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 202 107.01 - 113.75: 8403 113.75 - 120.49: 2188 120.49 - 127.23: 1768 127.23 - 133.96: 58 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C ALA A 31 " pdb=" CA ALA A 31 " pdb=" CB ALA A 31 " ideal model delta sigma weight residual 117.23 111.35 5.88 1.36e+00 5.41e-01 1.87e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.70 -5.00 1.80e+00 3.09e-01 7.73e+00 angle pdb=" N VAL A 83 " pdb=" CA VAL A 83 " pdb=" C VAL A 83 " ideal model delta sigma weight residual 112.29 110.01 2.28 9.40e-01 1.13e+00 5.90e+00 angle pdb=" CA ALA A 31 " pdb=" C ALA A 31 " pdb=" N PHE A 32 " ideal model delta sigma weight residual 119.98 118.01 1.97 8.50e-01 1.38e+00 5.38e+00 angle pdb=" C ILE B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta sigma weight residual 118.97 120.83 -1.86 1.04e+00 9.25e-01 3.21e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 2094 14.70 - 29.40: 216 29.40 - 44.10: 100 44.10 - 58.81: 42 58.81 - 73.51: 2 Dihedral angle restraints: 2454 sinusoidal: 1853 harmonic: 601 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -111.00 25.00 1 1.00e+01 1.00e-02 8.99e+00 dihedral pdb=" CB CYS N 198 " pdb=" SG CYS N 198 " pdb=" SG CYS N 218 " pdb=" CB CYS N 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.92 24.92 1 1.00e+01 1.00e-02 8.94e+00 dihedral pdb=" CB MET N 215 " pdb=" CG MET N 215 " pdb=" SD MET N 215 " pdb=" CE MET N 215 " ideal model delta sinusoidal sigma weight residual -180.00 -131.88 -48.12 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.055: 121 0.055 - 0.082: 33 0.082 - 0.110: 26 0.110 - 0.137: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 531 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 38 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 33 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 34 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 37 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 38 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.015 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 502 2.12 - 2.74: 11160 2.74 - 3.36: 19049 3.36 - 3.98: 23799 3.98 - 4.60: 35425 Nonbonded interactions: 89935 Sorted by model distance: nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.503 1.850 nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.509 1.850 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.536 1.850 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.536 1.850 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.850 ... (remaining 89930 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: 0.020 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 11.960 Find NCS groups from input model: 0.050 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:7.780 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 0.024 3510 Z= 0.115 Angle : 0.446 5.882 4772 Z= 0.241 Chirality : 0.037 0.137 534 Planarity : 0.004 0.047 625 Dihedral : 11.743 73.507 1334 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 2.67 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -0.68 (0.38), residues: 434 helix: -0.08 (0.30), residues: 280 sheet: -3.36 (0.65), residues: 9 loop : -0.74 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR B 145 PHE 0.004 0.001 PHE A 32 TRP 0.005 0.001 TRP B 117 HIS 0.002 0.000 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3510 Z= 0.170 Angle : 0.512 4.225 4772 Z= 0.271 Chirality : 0.044 0.146 534 Planarity : 0.004 0.036 625 Dihedral : 10.335 53.110 1334 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.53 % Allowed : 2.67 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 0.84 (0.39), residues: 434 helix: 0.96 (0.31), residues: 277 sheet: -2.38 (1.13), residues: 9 loop : 0.21 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.007 0.001 TYR A 130 PHE 0.009 0.001 PHE A 40 TRP 0.008 0.001 TRP N 184 HIS 0.003 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 8 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3510 Z= 0.228 Angle : 0.566 4.737 4772 Z= 0.306 Chirality : 0.043 0.147 534 Planarity : 0.005 0.048 625 Dihedral : 10.960 57.927 1334 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 5.08 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.38), residues: 434 helix: 0.33 (0.31), residues: 261 sheet: -2.14 (1.38), residues: 9 loop : 0.27 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.008 0.001 TYR B 169 PHE 0.005 0.001 PHE N 161 TRP 0.008 0.001 TRP B 117 HIS 0.003 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 30.0000 chunk 4 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 overall best weight: 4.0124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3510 Z= 0.089 Angle : 0.408 4.605 4772 Z= 0.196 Chirality : 0.041 0.162 534 Planarity : 0.004 0.036 625 Dihedral : 9.968 57.610 1334 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.07 % Allowed : 5.08 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 1.27 (0.39), residues: 434 helix: 1.15 (0.31), residues: 264 sheet: -1.80 (1.51), residues: 9 loop : 0.71 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.004 0.001 TYR B 169 PHE 0.004 0.001 PHE A 40 TRP 0.004 0.001 TRP B 117 HIS 0.002 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3510 Z= 0.244 Angle : 0.596 4.310 4772 Z= 0.334 Chirality : 0.044 0.155 534 Planarity : 0.005 0.046 625 Dihedral : 10.999 68.872 1334 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.94 % Allowed : 6.42 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -0.15 (0.37), residues: 434 helix: -0.27 (0.29), residues: 257 sheet: None (None), residues: 0 loop : 0.47 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.009 0.002 TYR B 169 PHE 0.011 0.002 PHE A 40 TRP 0.007 0.002 TRP B 117 HIS 0.006 0.002 HIS B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 40.0000 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.0070 chunk 36 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 overall best weight: 5.7406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3510 Z= 0.105 Angle : 0.430 4.217 4772 Z= 0.212 Chirality : 0.041 0.165 534 Planarity : 0.004 0.037 625 Dihedral : 10.133 64.330 1334 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.94 % Allowed : 4.81 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 0.89 (0.39), residues: 434 helix: 0.55 (0.31), residues: 251 sheet: None (None), residues: 0 loop : 0.95 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.005 0.001 TYR B 145 PHE 0.004 0.001 PHE N 168 TRP 0.003 0.001 TRP B 117 HIS 0.003 0.001 HIS A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 513.03 seconds wall clock time: 9 minutes 11.56 seconds (551.56 seconds total)