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/8sgt_40467.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.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=3.6 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.pdb" } resolution = 3.6 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= 0.056 sd= 0.109 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 30 5.16 5 C 4608 2.51 5 N 1145 2.21 5 O 1347 1.98 5 H 7044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "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: 14174 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 10724 Inner-chain residues flagged as termini: ['pdbres="SER A 73 "', 'pdbres="GLU A 97 "', 'pdbres="PHE A 223 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="LEU A 653 "', 'pdbres="GLU A 683 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 687} Modifications used: {'COO': 7, 'NH2': 1, 'NH3': 6} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1609 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 2.80, per 1000 atoms: 0.20 Number of scatterers: 14174 At special positions: 0 Unit cell: (121.18, 97.11, 146.91, 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 30 16.00 O 1347 8.00 N 1145 7.00 C 4608 6.00 H 7044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 4.61 Conformation dependent library (CDL) restraints added in 642.4 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 5.32 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: 7033 1.14 - 1.31: 1178 1.31 - 1.48: 3024 1.48 - 1.65: 3062 1.65 - 1.81: 43 Bond restraints: 14340 Sorted by residual: bond pdb=" N GLY A 848 " pdb=" H GLY A 848 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N LEU A 457 " pdb=" H LEU A 457 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N ILE A 59 " pdb=" H ILE A 59 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N VAL H 37 " pdb=" H VAL H 37 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N GLN A 826 " pdb=" H GLN A 826 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 14335 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 291 107.04 - 113.80: 16895 113.80 - 120.56: 4717 120.56 - 127.32: 3877 127.32 - 134.07: 82 Bond angle restraints: 25862 Sorted by residual: angle pdb=" N SER A 655 " pdb=" CA SER A 655 " pdb=" CB SER A 655 " ideal model delta sigma weight residual 114.17 111.16 3.01 1.14e+00 7.69e-01 6.98e+00 angle pdb=" C GLU L 39 " pdb=" N LYS L 40 " pdb=" CA LYS L 40 " ideal model delta sigma weight residual 121.92 125.16 -3.24 1.60e+00 3.91e-01 4.09e+00 angle pdb=" C GLU A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.32 117.11 4.21 2.10e+00 2.27e-01 4.01e+00 angle pdb=" C THR A 654 " pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 126.45 123.15 3.30 1.77e+00 3.19e-01 3.48e+00 angle pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " pdb=" CG ARG A 632 " ideal model delta sigma weight residual 114.10 117.51 -3.41 2.00e+00 2.50e-01 2.91e+00 ... (remaining 25857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 4512 16.74 - 33.49: 383 33.49 - 50.23: 130 50.23 - 66.98: 59 66.98 - 83.72: 14 Dihedral angle restraints: 5098 sinusoidal: 3565 harmonic: 1533 Sorted by residual: dihedral pdb=" CA GLU A 566 " pdb=" C GLU A 566 " pdb=" N ILE A 567 " pdb=" CA ILE A 567 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N THR H 61 " pdb=" CA THR H 61 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 675 0.030 - 0.060: 314 0.060 - 0.090: 84 0.090 - 0.121: 51 0.121 - 0.151: 16 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA ILE A 542 " pdb=" N ILE A 542 " pdb=" C ILE A 542 " pdb=" CB ILE A 542 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 641 " pdb=" N ILE A 641 " pdb=" C ILE A 641 " pdb=" CB ILE A 641 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1137 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 133 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 112 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 488 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 489 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.018 5.00e-02 4.00e+02 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 960 2.09 - 2.72: 21992 2.72 - 3.35: 39877 3.35 - 3.97: 55194 3.97 - 4.60: 80232 Nonbonded interactions: 198255 Sorted by model distance: nonbonded pdb=" O VAL A 430 " pdb=" HZ2 LYS A 438 " model vdw 1.468 1.850 nonbonded pdb=" OE1 GLU A 113 " pdb=" H GLU A 113 " model vdw 1.513 1.850 nonbonded pdb=" O THR A 135 " pdb=" HG SER A 139 " model vdw 1.517 1.850 nonbonded pdb=" O LEU A 55 " pdb=" HG SER A 58 " model vdw 1.526 1.850 nonbonded pdb=" O SER A 35 " pdb=" HZ2 LYS A 39 " model vdw 1.530 1.850 ... (remaining 198250 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: 0.090 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: 0.140 Extract box with map and model: 0.470 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:18.810 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 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 : 0.003 0.053 7296 Z= 0.169 Angle : 0.519 5.447 9920 Z= 0.289 Chirality : 0.042 0.151 1140 Planarity : 0.004 0.041 1249 Dihedral : 12.725 82.505 2534 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.92 (0.26), residues: 900 helix: -0.14 (0.27), residues: 314 sheet: -0.53 (0.32), residues: 251 loop : -0.92 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 595 TYR 0.012 0.001 TYR A 180 PHE 0.016 0.002 PHE A 553 TRP 0.007 0.001 TRP A 198 HIS 0.002 0.001 HIS A 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7296 Z= 0.281 Angle : 0.480 4.420 9920 Z= 0.257 Chirality : 0.050 0.202 1140 Planarity : 0.004 0.038 1249 Dihedral : 11.726 83.446 2534 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.05 (0.28), residues: 900 helix: 1.17 (0.28), residues: 321 sheet: -0.45 (0.32), residues: 255 loop : -0.56 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 527 TYR 0.013 0.001 TYR L 33 PHE 0.010 0.001 PHE A 553 TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 30.0000 chunk 64 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 18 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7296 Z= 0.218 Angle : 0.410 4.059 9920 Z= 0.216 Chirality : 0.052 0.175 1140 Planarity : 0.003 0.037 1249 Dihedral : 10.544 88.079 2534 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.49 (0.29), residues: 900 helix: 1.80 (0.29), residues: 321 sheet: -0.44 (0.33), residues: 256 loop : -0.40 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 595 TYR 0.009 0.001 TYR H 60 PHE 0.011 0.001 PHE L 88 TRP 0.010 0.001 TRP H 111 HIS 0.003 0.001 HIS A 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7296 Z= 0.150 Angle : 0.371 3.816 9920 Z= 0.193 Chirality : 0.050 0.169 1140 Planarity : 0.003 0.036 1249 Dihedral : 9.915 86.408 2534 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.78 (0.29), residues: 900 helix: 2.12 (0.29), residues: 317 sheet: -0.39 (0.33), residues: 258 loop : -0.19 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 595 TYR 0.007 0.001 TYR L 33 PHE 0.007 0.001 PHE A 507 TRP 0.009 0.001 TRP H 111 HIS 0.003 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 chunk 56 optimal weight: 0.0270 chunk 66 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7296 Z= 0.230 Angle : 0.422 4.379 9920 Z= 0.224 Chirality : 0.052 0.187 1140 Planarity : 0.003 0.035 1249 Dihedral : 9.773 84.416 2534 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.22 % Favored : 95.56 % Rotamer: Outliers : 0.13 % Allowed : 2.21 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.68 (0.29), residues: 900 helix: 2.17 (0.29), residues: 319 sheet: -0.57 (0.34), residues: 249 loop : -0.32 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 595 TYR 0.012 0.001 TYR L 33 PHE 0.013 0.001 PHE L 45 TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 50.0000 chunk 42 optimal weight: 0.3980 chunk 31 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 50.0000 overall best weight: 7.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7296 Z= 0.247 Angle : 0.430 4.859 9920 Z= 0.227 Chirality : 0.050 0.174 1140 Planarity : 0.003 0.034 1249 Dihedral : 9.804 75.179 2534 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.39 % Allowed : 2.73 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.72 (0.29), residues: 900 helix: 2.27 (0.29), residues: 312 sheet: -0.64 (0.34), residues: 240 loop : -0.25 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.011 0.001 TYR L 33 PHE 0.010 0.001 PHE L 45 TRP 0.012 0.001 TRP H 111 HIS 0.004 0.001 HIS A 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 616.36 seconds wall clock time: 11 minutes 4.57 seconds (664.57 seconds total)