Starting phenix.real_space_refine on Sun May 19 16:32:01 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: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.3 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 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { 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= 0.095 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: 0.01s 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: 2.10, per 1000 atoms: 0.33 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: 3.42 Conformation dependent library (CDL) restraints added in 645.8 milliseconds Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 9.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.502A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.333A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'L' and resid 81 through 84 No H-bonds generated for 'chain 'L' and resid 81 through 84' Processing sheet with id= A, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.509A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.754A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= D, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.031A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 114 through 116 removed outlier: 3.583A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.731A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.856A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 98 through 100 removed outlier: 6.369A pdb=" N GLN L 39 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS L 41 " --> pdb=" O PHE L 46 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE L 46 " --> pdb=" O LYS L 41 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.02 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: 289 2.07 - 2.70: 9315 2.70 - 3.33: 17483 3.33 - 3.97: 24689 3.97 - 4.60: 35702 Nonbonded interactions: 87478 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 87473 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: 0.070 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.350 Find NCS groups from input model: 0.090 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:8.760 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- 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= 0.174 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3368 Z= 0.244 Angle : 0.543 5.184 4588 Z= 0.286 Chirality : 0.057 0.197 498 Planarity : 0.003 0.033 593 Dihedral : 11.515 88.855 1181 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.43 % Favored : 92.33 % Rotamer: Outliers : 0.85 % Allowed : 4.51 % 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: -2.41 (0.38), residues: 417 helix: -2.50 (0.71), residues: 32 sheet: -1.14 (0.41), residues: 143 loop : -1.77 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 97 TYR 0.007 0.001 TYR A 380 PHE 0.008 0.001 PHE A 490 TRP 0.006 0.001 TRP H 52 HIS 0.001 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 overall best weight: 10.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3368 Z= 0.345 Angle : 0.568 4.805 4588 Z= 0.303 Chirality : 0.061 0.190 498 Planarity : 0.004 0.047 593 Dihedral : 11.566 85.836 1181 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 2.64 % Allowed : 11.75 % Favored : 85.61 % Rotamer: Outliers : 1.97 % Allowed : 6.48 % Favored : 91.55 % 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: -4.09 (0.34), residues: 417 helix: -3.38 (0.65), residues: 32 sheet: -2.01 (0.40), residues: 137 loop : -3.17 (0.32), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.011 0.001 TYR A 380 PHE 0.009 0.001 PHE L 64 TRP 0.008 0.002 TRP A 436 HIS 0.001 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3368 Z= 0.288 Angle : 0.520 4.537 4588 Z= 0.275 Chirality : 0.058 0.192 498 Planarity : 0.003 0.037 593 Dihedral : 11.365 84.730 1181 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 1.68 % Allowed : 13.43 % Favored : 84.89 % Rotamer: Outliers : 1.97 % Allowed : 5.07 % Favored : 92.96 % 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 (0.35), residues: 417 helix: -3.56 (0.57), residues: 32 sheet: -2.22 (0.37), residues: 155 loop : -3.33 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR A 453 PHE 0.009 0.001 PHE L 64 TRP 0.005 0.001 TRP H 47 HIS 0.001 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- 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: 20.0000 chunk 35 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 3368 Z= 0.330 Angle : 0.533 4.841 4588 Z= 0.284 Chirality : 0.059 0.191 498 Planarity : 0.004 0.041 593 Dihedral : 11.437 82.877 1181 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 2.64 % Allowed : 14.87 % Favored : 82.49 % Rotamer: Outliers : 1.97 % Allowed : 7.61 % Favored : 90.42 % 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: -4.84 (0.34), residues: 417 helix: -3.92 (0.43), residues: 32 sheet: -2.46 (0.37), residues: 154 loop : -3.77 (0.33), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.009 0.001 TYR A 380 PHE 0.009 0.001 PHE A 490 TRP 0.009 0.002 TRP A 436 HIS 0.002 0.001 HIS L 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3368 Z= 0.313 Angle : 0.522 4.674 4588 Z= 0.277 Chirality : 0.058 0.191 498 Planarity : 0.004 0.036 593 Dihedral : 11.417 81.408 1181 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 2.64 % Allowed : 15.59 % Favored : 81.77 % Rotamer: Outliers : 1.97 % Allowed : 9.30 % Favored : 88.73 % 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: -4.92 (0.34), residues: 417 helix: -4.32 (0.31), residues: 33 sheet: -2.43 (0.38), residues: 154 loop : -3.83 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 380 PHE 0.009 0.001 PHE A 490 TRP 0.007 0.001 TRP L 37 HIS 0.002 0.001 HIS L 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 219.47 seconds wall clock time: 4 minutes 23.35 seconds (263.35 seconds total)