Starting phenix.real_space_refine on Sun May 19 16:31:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False resolution=3.99 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1g_18810.pdb" } resolution = 3.99 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { secondary_structure { enabled = False } c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.079 sd= 0.315 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 57 5.16 5 C 5307 2.51 5 N 1431 2.21 5 O 1577 1.98 5 H 8296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 54": "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: 16668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11116 Inner-chain residues flagged as termini: ['pdbres="PHE A 167 "', 'pdbres="VAL A 234 "'] Classifications: {'peptide': 681} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2394 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3158 Classifications: {'peptide': 202} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 186} Time building chain proxies: 3.07, per 1000 atoms: 0.18 Number of scatterers: 16668 At special positions: 0 Unit cell: (99.12, 110.88, 122.64, 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 57 16.00 O 1577 8.00 N 1431 7.00 C 5307 6.00 H 8296 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: 4.58 Conformation dependent library (CDL) restraints added in 643.8 milliseconds Time building geometry restraints manager: 5.27 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: 8267 1.14 - 1.31: 1437 1.31 - 1.48: 3383 1.48 - 1.64: 3673 1.64 - 1.81: 85 Bond restraints: 16845 Sorted by residual: bond pdb=" N ARG A 424 " pdb=" H ARG A 424 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N THR A 741 " pdb=" H THR A 741 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N THR A 842 " pdb=" H THR A 842 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N LEU A 849 " pdb=" H LEU A 849 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 16840 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.28: 175 105.28 - 112.46: 19201 112.46 - 119.64: 4530 119.64 - 126.82: 6424 126.82 - 134.00: 88 Bond angle restraints: 30418 Sorted by residual: angle pdb=" N GLN B 114 " pdb=" CA GLN B 114 " pdb=" CB GLN B 114 " ideal model delta sigma weight residual 113.65 110.17 3.48 1.47e+00 4.63e-01 5.59e+00 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 110.23 108.14 2.09 1.04e+00 9.25e-01 4.05e+00 angle pdb=" HE2 MET B 144 " pdb=" CE MET B 144 " pdb=" HE3 MET B 144 " ideal model delta sigma weight residual 110.00 115.62 -5.62 3.00e+00 1.11e-01 3.50e+00 angle pdb=" CA VAL A 740 " pdb=" C VAL A 740 " pdb=" N THR A 741 " ideal model delta sigma weight residual 116.60 119.20 -2.60 1.45e+00 4.76e-01 3.21e+00 angle pdb=" C PRO A 745 " pdb=" N LEU A 746 " pdb=" CA LEU A 746 " ideal model delta sigma weight residual 120.79 123.28 -2.49 1.39e+00 5.18e-01 3.20e+00 ... (remaining 30413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 5422 16.91 - 33.82: 387 33.82 - 50.73: 133 50.73 - 67.64: 37 67.64 - 84.55: 5 Dihedral angle restraints: 5984 sinusoidal: 4370 harmonic: 1614 Sorted by residual: dihedral pdb=" CA CYS C 229 " pdb=" CB CYS C 229 " pdb=" SG CYS C 229 " pdb=" HG CYS C 229 " ideal model delta sinusoidal sigma weight residual -60.00 -119.95 59.95 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG C 209 " pdb=" CB ARG C 209 " pdb=" CG ARG C 209 " pdb=" CD ARG C 209 " ideal model delta sinusoidal sigma weight residual 60.00 116.28 -56.28 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " pdb=" CG ARG A 155 " pdb=" CD ARG A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -114.37 54.37 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 828 0.030 - 0.061: 307 0.061 - 0.091: 74 0.091 - 0.121: 41 0.121 - 0.152: 10 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1257 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO A 307 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.121 9.50e-02 1.11e+02 4.04e-02 1.81e+00 pdb=" NE ARG A 734 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 288 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ILE A 288 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE A 288 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 289 " 0.007 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 873 2.06 - 2.70: 23935 2.70 - 3.33: 50047 3.33 - 3.97: 64139 3.97 - 4.60: 95666 Nonbonded interactions: 234660 Sorted by model distance: nonbonded pdb="HE21 GLN A 410 " pdb=" O GLU A 415 " model vdw 1.428 1.850 nonbonded pdb=" H SER B 118 " pdb=" OE1 GLU B 121 " model vdw 1.514 1.850 nonbonded pdb=" O LEU A 770 " pdb=" HG1 THR A 774 " model vdw 1.523 1.850 nonbonded pdb=" OE1 GLU A 860 " pdb=" HE ARG A 861 " model vdw 1.565 1.850 nonbonded pdb="HH12 ARG A 424 " pdb=" O PHE A 467 " model vdw 1.569 1.850 ... (remaining 234655 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: 0.000 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: 0.170 Extract box with map and model: 0.600 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.470 Find NCS groups from input model: 0.110 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:19.820 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 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 0.035 8549 Z= 0.121 Angle : 0.503 4.124 11554 Z= 0.280 Chirality : 0.038 0.152 1260 Planarity : 0.005 0.053 1505 Dihedral : 10.788 77.455 3280 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.21 % Allowed : 2.44 % Favored : 97.35 % 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: -0.56 (0.25), residues: 1017 helix: -0.35 (0.21), residues: 483 sheet: -0.58 (0.47), residues: 117 loop : -0.07 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.017 0.001 TYR A 494 PHE 0.017 0.001 PHE A 730 TRP 0.011 0.001 TRP A 791 HIS 0.004 0.001 HIS C 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8549 Z= 0.202 Angle : 0.619 6.810 11554 Z= 0.330 Chirality : 0.050 0.204 1260 Planarity : 0.005 0.045 1505 Dihedral : 10.117 75.544 3280 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.70 % Favored : 86.82 % Rotamer: Outliers : 0.53 % Allowed : 2.12 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.21), residues: 1017 helix: -3.74 (0.15), residues: 480 sheet: -1.84 (0.47), residues: 117 loop : -1.79 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.011 0.002 TYR B 86 PHE 0.018 0.002 PHE B 52 TRP 0.003 0.001 TRP C 146 HIS 0.004 0.001 HIS A 655 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 120.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 8549 Z= 0.311 Angle : 0.742 7.173 11554 Z= 0.397 Chirality : 0.057 0.256 1260 Planarity : 0.006 0.065 1505 Dihedral : 12.112 92.929 3280 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 26.48 Ramachandran Plot: Outliers : 6.19 % Allowed : 20.65 % Favored : 73.16 % Rotamer: Outliers : 1.80 % Allowed : 4.99 % Favored : 93.21 % 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: -6.06 (0.19), residues: 1017 helix: -4.73 (0.11), residues: 452 sheet: -2.87 (0.45), residues: 108 loop : -3.42 (0.24), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 418 TYR 0.019 0.002 TYR A 494 PHE 0.017 0.002 PHE A 730 TRP 0.009 0.002 TRP A 791 HIS 0.009 0.002 HIS B 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 60.0000 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 120.0000 chunk 71 optimal weight: 20.0000 overall best weight: 11.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8549 Z= 0.198 Angle : 0.557 4.938 11554 Z= 0.297 Chirality : 0.050 0.179 1260 Planarity : 0.004 0.055 1505 Dihedral : 11.663 77.989 3280 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 2.75 % Allowed : 17.21 % Favored : 80.04 % Rotamer: Outliers : 1.59 % Allowed : 5.84 % Favored : 92.57 % 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: -5.75 (0.20), residues: 1017 helix: -4.47 (0.13), residues: 432 sheet: -3.15 (0.46), residues: 93 loop : -3.26 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.010 0.002 TYR A 748 PHE 0.008 0.002 PHE A 601 TRP 0.005 0.001 TRP A 600 HIS 0.006 0.001 HIS C 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 80.0000 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 90.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8549 Z= 0.197 Angle : 0.562 6.245 11554 Z= 0.298 Chirality : 0.051 0.184 1260 Planarity : 0.005 0.063 1505 Dihedral : 11.449 86.443 3280 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 4.52 % Allowed : 18.58 % Favored : 76.89 % Rotamer: Outliers : 1.70 % Allowed : 6.05 % Favored : 92.25 % 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: -6.05 (0.19), residues: 1017 helix: -4.58 (0.12), residues: 421 sheet: -3.65 (0.45), residues: 91 loop : -3.55 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 138 TYR 0.013 0.002 TYR A 638 PHE 0.020 0.002 PHE B 54 TRP 0.009 0.001 TRP A 791 HIS 0.006 0.001 HIS C 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 92 optimal weight: 50.0000 chunk 51 optimal weight: 70.0000 chunk 90 optimal weight: 50.0000 chunk 100 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.8206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8549 Z= 0.279 Angle : 0.714 7.117 11554 Z= 0.390 Chirality : 0.055 0.203 1260 Planarity : 0.006 0.079 1505 Dihedral : 13.081 85.147 3280 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 37.35 Ramachandran Plot: Outliers : 9.64 % Allowed : 28.12 % Favored : 62.24 % Rotamer: Outliers : 3.82 % Allowed : 7.11 % Favored : 89.07 % 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: -6.85 (0.18), residues: 1017 helix: -5.07 (0.10), residues: 392 sheet: -4.08 (0.48), residues: 80 loop : -4.32 (0.21), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 424 TYR 0.016 0.002 TYR B 39 PHE 0.021 0.002 PHE B 54 TRP 0.007 0.002 TRP B 139 HIS 0.009 0.002 HIS C 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 379.84 seconds wall clock time: 7 minutes 29.98 seconds (449.98 seconds total)