Starting phenix.real_space_refine on Sun May 19 17:06:25 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- resolution=3.3 run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False overwrite=true nproc=50 max_reasonable_bond_distance=500 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7k9i_22749.pdb" } resolution = 3.3 nproc = 50 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 max_reasonable_bond_distance = 500 } output { overwrite = true } 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= 0.095 sd= 0.238 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 14 5.16 5 C 2087 2.51 5 N 553 2.21 5 O 630 1.98 5 H 3157 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: 6441 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3007 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1835 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1599 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Time building chain proxies: 0.97, per 1000 atoms: 0.15 Number of scatterers: 6441 At special positions: 0 Unit cell: (67.1, 88, 89.1, 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 14 16.00 O 630 8.00 N 553 7.00 C 2087 6.00 H 3157 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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: 1.09 Conformation dependent library (CDL) restraints added in 198.9 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3157 1.15 - 1.32: 530 1.32 - 1.49: 1488 1.49 - 1.66: 1334 1.66 - 1.83: 16 Bond restraints: 6525 Sorted by residual: bond pdb=" N ARG A 355 " pdb=" H ARG A 355 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N ASP A 405 " pdb=" H ASP A 405 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N ASN L 55 " pdb=" H ASN L 55 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N CYS H 22 " pdb=" H CYS H 22 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N THR L 21 " pdb=" H THR L 21 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 ... (remaining 6520 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.39: 282 107.39 - 114.07: 7372 114.07 - 120.75: 2255 120.75 - 127.43: 1758 127.43 - 134.10: 39 Bond angle restraints: 11706 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 125.66 130.28 -4.62 1.85e+00 2.92e-01 6.23e+00 angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 119.71 -5.31 2.30e+00 1.89e-01 5.33e+00 angle pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta sigma weight residual 119.99 122.43 -2.44 1.13e+00 7.83e-01 4.65e+00 angle pdb=" N GLY L 52 " pdb=" CA GLY L 52 " pdb=" C GLY L 52 " ideal model delta sigma weight residual 115.30 112.40 2.90 1.44e+00 4.82e-01 4.05e+00 angle pdb=" C TYR H 94 " pdb=" N CYS H 95 " pdb=" CA CYS H 95 " ideal model delta sigma weight residual 121.42 124.19 -2.77 1.43e+00 4.89e-01 3.76e+00 ... (remaining 11701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2107 17.73 - 35.46: 199 35.46 - 53.20: 51 53.20 - 70.93: 13 70.93 - 88.66: 4 Dihedral angle restraints: 2374 sinusoidal: 1656 harmonic: 718 Sorted by residual: dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.27 -30.27 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 67.28 25.72 1 1.00e+01 1.00e-02 9.51e+00 ... (remaining 2371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 295 0.031 - 0.061: 129 0.061 - 0.092: 41 0.092 - 0.122: 29 0.122 - 0.153: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE L 77 " pdb=" N ILE L 77 " pdb=" C ILE L 77 " pdb=" CB ILE L 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 495 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO L 42 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO H 40 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.075 9.50e-02 1.11e+02 2.54e-02 9.74e-01 pdb=" NE ARG A 355 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 355 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 355 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 355 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 356 2.07 - 2.70: 9329 2.70 - 3.33: 17564 3.33 - 3.97: 24837 3.97 - 4.60: 35797 Nonbonded interactions: 87883 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" HG1 THR A 523 " model vdw 1.436 1.850 nonbonded pdb=" HZ2 LYS H 64 " pdb=" O SER H 84 " model vdw 1.478 1.850 nonbonded pdb="HH12 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.506 1.850 nonbonded pdb=" O THR H 53 " pdb=" HZ3 LYS H 71 " model vdw 1.515 1.850 nonbonded pdb=" HE1 TRP H 52 " pdb=" OD1 ASN H 58 " model vdw 1.523 1.850 ... (remaining 87878 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: 0.010 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: 0.030 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.030 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:3.900 Internal consistency checks: 0.000 Total: 9.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 0.026 3368 Z= 0.181 Angle : 0.585 5.986 4588 Z= 0.318 Chirality : 0.044 0.153 498 Planarity : 0.004 0.037 593 Dihedral : 11.937 88.662 1181 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.00 % Favored : 93.76 % Rotamer: Outliers : 0.85 % Allowed : 3.94 % Favored : 95.21 % 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: -1.60 (0.38), residues: 417 helix: -2.37 (0.67), residues: 32 sheet: -0.54 (0.42), residues: 143 loop : -1.19 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.009 0.001 TYR A 423 PHE 0.008 0.001 PHE A 400 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3368 Z= 0.263 Angle : 0.504 4.844 4588 Z= 0.258 Chirality : 0.057 0.178 498 Planarity : 0.003 0.032 593 Dihedral : 11.563 89.248 1181 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.85 % Allowed : 3.66 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.39), residues: 417 helix: -1.92 (0.74), residues: 32 sheet: -0.34 (0.43), residues: 143 loop : -1.00 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.008 0.001 TYR A 489 PHE 0.010 0.001 PHE A 490 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 4.4986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3368 Z= 0.184 Angle : 0.458 4.471 4588 Z= 0.231 Chirality : 0.057 0.176 498 Planarity : 0.003 0.031 593 Dihedral : 10.988 89.349 1181 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 3.66 % Favored : 95.21 % 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: -0.89 (0.40), residues: 417 helix: -1.77 (0.77), residues: 33 sheet: -0.01 (0.44), residues: 141 loop : -0.73 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR A 423 PHE 0.008 0.001 PHE A 490 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 7.1190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3368 Z= 0.253 Angle : 0.470 4.763 4588 Z= 0.241 Chirality : 0.057 0.177 498 Planarity : 0.003 0.035 593 Dihedral : 10.895 87.625 1181 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.41 % Allowed : 3.38 % Favored : 95.21 % 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: -0.97 (0.40), residues: 417 helix: -1.84 (0.76), residues: 33 sheet: 0.18 (0.45), residues: 135 loop : -0.95 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR A 380 PHE 0.009 0.001 PHE A 490 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3368 Z= 0.250 Angle : 0.473 4.676 4588 Z= 0.243 Chirality : 0.057 0.174 498 Planarity : 0.003 0.035 593 Dihedral : 10.846 86.911 1181 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.41 % Allowed : 5.07 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.40), residues: 417 helix: -2.00 (0.74), residues: 33 sheet: 0.09 (0.45), residues: 135 loop : -0.92 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR A 380 PHE 0.009 0.001 PHE A 490 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS L 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 overall best weight: 2.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3368 Z= 0.127 Angle : 0.417 4.484 4588 Z= 0.206 Chirality : 0.055 0.174 498 Planarity : 0.003 0.030 593 Dihedral : 10.497 87.249 1181 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.41 % Allowed : 3.94 % Favored : 94.65 % 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: -0.83 (0.41), residues: 417 helix: -1.84 (0.77), residues: 33 sheet: -0.00 (0.43), residues: 150 loop : -0.66 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR A 423 PHE 0.009 0.001 PHE A 490 TRP 0.005 0.001 TRP H 47 HIS 0.001 0.000 HIS L 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 349.62 seconds wall clock time: 6 minutes 8.24 seconds (368.24 seconds total)