Starting phenix.real_space_refine on Tue Sep 24 04:36:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgz_45589/09_2024/9cgz_45589_neut.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.001 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 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.66, per 1000 atoms: 0.68 Number of scatterers: 6822 At special positions: 0 Unit cell: (146.28, 76.32, 36.04, 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 6 16.00 O 624 8.00 N 606 7.00 C 2106 6.00 H 3480 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 - 3.00 Amino acid : True - 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: 1.61 Conformation dependent library (CDL) restraints added in 592.1 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.948A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.539A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.560A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.621A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.962A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.619A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.714A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.463A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY F 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE D 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.615A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375 79 hydrogen bonds defined for protein. 237 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: 2.19 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3474 1.12 - 1.29: 558 1.29 - 1.47: 1055 1.47 - 1.64: 1783 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N GLU E 338 " pdb=" H GLU E 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NH1 ARG A 349 " pdb="HH12 ARG A 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU D 342 " pdb=" H GLU D 342 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE F 360 " pdb=" H ILE F 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CZ PHE C 346 " pdb=" HZ PHE C 346 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 10221 2.34 - 4.68: 1746 4.68 - 7.01: 528 7.01 - 9.35: 45 9.35 - 11.69: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 2742 16.10 - 32.20: 230 32.20 - 48.31: 86 48.31 - 64.41: 98 64.41 - 80.51: 12 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA GLY D 365 " pdb=" C GLY D 365 " pdb=" N GLY D 366 " pdb=" CA GLY D 366 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 286 0.070 - 0.140: 178 0.140 - 0.210: 46 0.210 - 0.280: 5 0.280 - 0.350: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS F 369 " pdb=" N LYS F 369 " pdb=" C LYS F 369 " pdb=" CB LYS F 369 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.140 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE E 346 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " 0.053 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " -0.012 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " -0.138 2.00e-02 2.50e+03 5.20e-02 8.10e+01 pdb=" CG PHE C 346 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE C 346 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE C 346 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE C 346 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE C 346 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.085 2.00e-02 2.50e+03 4.96e-02 5.53e+01 pdb=" CG HIS C 330 " -0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 HIS C 330 " 0.056 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 576 2.20 - 2.80: 12440 2.80 - 3.40: 17545 3.40 - 4.00: 24228 4.00 - 4.60: 33709 Nonbonded interactions: 88498 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.608 2.450 ... (remaining 88493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.620 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.290 Find NCS groups from input model: 0.170 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 : 0.011 0.040 3396 Z= 0.724 Angle : 1.914 6.574 4548 Z= 1.255 Chirality : 0.087 0.350 516 Planarity : 0.010 0.055 576 Dihedral : 12.927 80.509 1296 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.17 % Allowed : 6.81 % Favored : 92.02 % Rotamer: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.53 % 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: -2.13 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS F 362 PHE 0.090 0.015 PHE E 346 TYR 0.084 0.026 TYR D 310 ARG 0.008 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7713 (tttt) cc_final: 0.6490 (tmmt) REVERT: A 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7358 (ttmt) REVERT: A 331 LYS cc_start: 0.7570 (mttm) cc_final: 0.7355 (mtpp) REVERT: A 338 GLU cc_start: 0.7402 (tt0) cc_final: 0.7191 (tt0) REVERT: A 340 LYS cc_start: 0.8213 (mttt) cc_final: 0.7795 (mmtp) REVERT: B 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7625 (tttt) REVERT: B 338 GLU cc_start: 0.7653 (tt0) cc_final: 0.7101 (mm-30) REVERT: B 369 LYS cc_start: 0.7747 (mttt) cc_final: 0.7202 (mmtm) REVERT: C 311 LYS cc_start: 0.7102 (tttt) cc_final: 0.6753 (ttmt) REVERT: C 321 LYS cc_start: 0.7083 (tttt) cc_final: 0.6876 (ttmt) REVERT: C 327 ASN cc_start: 0.7483 (m-40) cc_final: 0.7066 (t0) REVERT: C 338 GLU cc_start: 0.6915 (tt0) cc_final: 0.6652 (tt0) REVERT: C 340 LYS cc_start: 0.7572 (mttt) cc_final: 0.7241 (mtmt) REVERT: D 311 LYS cc_start: 0.7860 (tttt) cc_final: 0.7240 (tttp) REVERT: D 321 LYS cc_start: 0.7332 (tttt) cc_final: 0.6077 (tmtm) REVERT: D 327 ASN cc_start: 0.7511 (m-40) cc_final: 0.7145 (t0) REVERT: D 338 GLU cc_start: 0.6957 (tt0) cc_final: 0.6603 (tp30) REVERT: D 353 LYS cc_start: 0.7437 (mttt) cc_final: 0.7003 (mttm) REVERT: E 311 LYS cc_start: 0.7069 (tttt) cc_final: 0.6567 (mmtt) REVERT: E 353 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6772 (ttpp) REVERT: E 356 SER cc_start: 0.8514 (p) cc_final: 0.7946 (t) REVERT: E 358 ASP cc_start: 0.7430 (m-30) cc_final: 0.6988 (m-30) REVERT: F 315 LEU cc_start: 0.8124 (mp) cc_final: 0.7855 (mt) REVERT: F 321 LYS cc_start: 0.7239 (tttt) cc_final: 0.6859 (ttpt) REVERT: F 353 LYS cc_start: 0.7324 (mttt) cc_final: 0.7009 (mtmt) REVERT: F 356 SER cc_start: 0.8475 (p) cc_final: 0.7984 (p) REVERT: F 358 ASP cc_start: 0.7520 (m-30) cc_final: 0.7232 (m-30) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 2.5475 time to fit residues: 321.4486 Evaluate side-chains 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN B 336 GLN C 351 GLN D 336 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3396 Z= 0.265 Angle : 0.661 6.680 4548 Z= 0.347 Chirality : 0.050 0.134 516 Planarity : 0.003 0.020 576 Dihedral : 8.003 54.369 447 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.82 % Allowed : 15.10 % Favored : 83.07 % 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: -2.04 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.006 0.001 PHE E 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7684 (tttt) cc_final: 0.7463 (tttt) REVERT: A 321 LYS cc_start: 0.7883 (tttt) cc_final: 0.7508 (mtpp) REVERT: A 338 GLU cc_start: 0.7771 (tt0) cc_final: 0.7070 (tm-30) REVERT: A 340 LYS cc_start: 0.8318 (mttt) cc_final: 0.7805 (mttt) REVERT: B 321 LYS cc_start: 0.7888 (tttt) cc_final: 0.7619 (tttt) REVERT: B 340 LYS cc_start: 0.8149 (mttt) cc_final: 0.7927 (mmtp) REVERT: B 369 LYS cc_start: 0.7729 (mttt) cc_final: 0.7157 (mmtm) REVERT: C 311 LYS cc_start: 0.7107 (tttt) cc_final: 0.6603 (ttmt) REVERT: C 331 LYS cc_start: 0.7572 (mttm) cc_final: 0.7354 (mtmt) REVERT: C 338 GLU cc_start: 0.6931 (tt0) cc_final: 0.6601 (tt0) REVERT: C 340 LYS cc_start: 0.7740 (mttt) cc_final: 0.7289 (mtmt) REVERT: C 342 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6975 (mm-30) REVERT: D 311 LYS cc_start: 0.7452 (tttt) cc_final: 0.6988 (tttm) REVERT: D 321 LYS cc_start: 0.7158 (tttt) cc_final: 0.6430 (mtmt) REVERT: D 338 GLU cc_start: 0.7369 (tt0) cc_final: 0.6898 (tm-30) REVERT: D 340 LYS cc_start: 0.7902 (mttt) cc_final: 0.7628 (mttt) REVERT: D 342 GLU cc_start: 0.7663 (mp0) cc_final: 0.6242 (mp0) REVERT: D 353 LYS cc_start: 0.7398 (mttt) cc_final: 0.7027 (mttm) REVERT: E 343 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7523 (mtpp) REVERT: E 353 LYS cc_start: 0.7447 (ttmt) cc_final: 0.6976 (ttpp) REVERT: F 315 LEU cc_start: 0.8131 (mp) cc_final: 0.7858 (mt) REVERT: F 353 LYS cc_start: 0.7204 (mttt) cc_final: 0.6876 (mtmt) REVERT: F 356 SER cc_start: 0.8307 (p) cc_final: 0.7776 (p) REVERT: F 358 ASP cc_start: 0.7633 (m-30) cc_final: 0.7425 (m-30) REVERT: F 369 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7417 (mttm) outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 2.2965 time to fit residues: 252.6458 Evaluate side-chains 85 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3396 Z= 0.202 Angle : 0.603 4.486 4548 Z= 0.317 Chirality : 0.050 0.127 516 Planarity : 0.004 0.028 576 Dihedral : 6.725 21.014 444 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.34 % Allowed : 17.71 % Favored : 79.95 % 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: -2.26 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.010 0.001 PHE E 346 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.609 Fit side-chains REVERT: A 321 LYS cc_start: 0.7565 (tttt) cc_final: 0.7316 (mtpp) REVERT: A 338 GLU cc_start: 0.7974 (tt0) cc_final: 0.7199 (tm-30) REVERT: A 340 LYS cc_start: 0.8276 (mttt) cc_final: 0.7792 (mttt) REVERT: A 342 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6462 (pm20) REVERT: A 370 LYS cc_start: 0.7792 (tttm) cc_final: 0.7592 (tptp) REVERT: B 340 LYS cc_start: 0.8202 (mttt) cc_final: 0.7957 (mmtp) REVERT: B 369 LYS cc_start: 0.7861 (mttt) cc_final: 0.7320 (mttp) REVERT: C 311 LYS cc_start: 0.6994 (tttt) cc_final: 0.6451 (ttmt) REVERT: C 331 LYS cc_start: 0.7411 (mttm) cc_final: 0.7201 (mtmt) REVERT: C 338 GLU cc_start: 0.7203 (tt0) cc_final: 0.6779 (tt0) REVERT: C 340 LYS cc_start: 0.7656 (mttt) cc_final: 0.7334 (mtmt) REVERT: C 342 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7188 (mm-30) REVERT: D 311 LYS cc_start: 0.7496 (tttt) cc_final: 0.7053 (tttp) REVERT: D 321 LYS cc_start: 0.7215 (tttt) cc_final: 0.6825 (ttmt) REVERT: D 340 LYS cc_start: 0.7787 (mttt) cc_final: 0.7581 (mttm) REVERT: D 342 GLU cc_start: 0.7706 (mp0) cc_final: 0.7325 (mp0) REVERT: D 348 ASP cc_start: 0.7480 (t0) cc_final: 0.7253 (t0) REVERT: D 353 LYS cc_start: 0.7317 (mttt) cc_final: 0.6950 (mttt) REVERT: E 325 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7871 (tp) REVERT: E 353 LYS cc_start: 0.7494 (ttmt) cc_final: 0.6939 (ttpp) REVERT: E 356 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8210 (t) REVERT: F 315 LEU cc_start: 0.8127 (mp) cc_final: 0.7832 (mt) REVERT: F 321 LYS cc_start: 0.7751 (tttt) cc_final: 0.7214 (ttmt) REVERT: F 343 LYS cc_start: 0.7759 (mptt) cc_final: 0.6254 (tppt) REVERT: F 344 LEU cc_start: 0.8585 (mt) cc_final: 0.8374 (mp) REVERT: F 351 GLN cc_start: 0.7279 (mt0) cc_final: 0.6989 (mt0) REVERT: F 353 LYS cc_start: 0.7199 (mttt) cc_final: 0.6901 (mtpt) REVERT: F 356 SER cc_start: 0.8380 (p) cc_final: 0.8004 (p) REVERT: F 358 ASP cc_start: 0.7635 (m-30) cc_final: 0.7399 (m-30) REVERT: F 369 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7272 (mttm) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 2.4786 time to fit residues: 237.1597 Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3396 Z= 0.181 Angle : 0.553 4.135 4548 Z= 0.291 Chirality : 0.050 0.125 516 Planarity : 0.003 0.027 576 Dihedral : 6.337 19.681 444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.86 % Allowed : 17.71 % Favored : 79.43 % 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: -2.30 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.007 0.001 PHE C 346 TYR 0.012 0.003 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.581 Fit side-chains REVERT: A 321 LYS cc_start: 0.7647 (tttt) cc_final: 0.7360 (mtpp) REVERT: A 338 GLU cc_start: 0.8010 (tt0) cc_final: 0.7232 (tm-30) REVERT: A 340 LYS cc_start: 0.8207 (mttt) cc_final: 0.7778 (mttt) REVERT: B 340 LYS cc_start: 0.8167 (mttt) cc_final: 0.7962 (mmtp) REVERT: B 369 LYS cc_start: 0.7915 (mttt) cc_final: 0.7425 (mttp) REVERT: C 311 LYS cc_start: 0.7071 (tttt) cc_final: 0.6482 (ttmt) REVERT: C 331 LYS cc_start: 0.7444 (mttm) cc_final: 0.7103 (mtmt) REVERT: C 338 GLU cc_start: 0.7289 (tt0) cc_final: 0.6833 (tt0) REVERT: C 340 LYS cc_start: 0.7695 (mttt) cc_final: 0.7410 (mtmt) REVERT: C 342 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 311 LYS cc_start: 0.7450 (tttt) cc_final: 0.7010 (tttp) REVERT: D 321 LYS cc_start: 0.7224 (tttt) cc_final: 0.6713 (mtmt) REVERT: D 342 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: D 356 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7414 (t) REVERT: E 325 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7938 (tp) REVERT: E 353 LYS cc_start: 0.7438 (ttmt) cc_final: 0.6915 (ttpp) REVERT: E 356 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8242 (t) REVERT: E 358 ASP cc_start: 0.7389 (m-30) cc_final: 0.7067 (m-30) REVERT: F 315 LEU cc_start: 0.8111 (mp) cc_final: 0.7824 (mt) REVERT: F 321 LYS cc_start: 0.7770 (tttt) cc_final: 0.7130 (ttmt) REVERT: F 343 LYS cc_start: 0.7770 (mptt) cc_final: 0.6370 (tppt) REVERT: F 344 LEU cc_start: 0.8585 (mt) cc_final: 0.8250 (mp) REVERT: F 345 ASP cc_start: 0.7273 (t0) cc_final: 0.6499 (m-30) REVERT: F 351 GLN cc_start: 0.7312 (mt0) cc_final: 0.7031 (mt0) REVERT: F 353 LYS cc_start: 0.7139 (mttt) cc_final: 0.6818 (mtpt) REVERT: F 356 SER cc_start: 0.8460 (p) cc_final: 0.7915 (p) REVERT: F 358 ASP cc_start: 0.7624 (m-30) cc_final: 0.7424 (m-30) REVERT: F 369 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7222 (mttm) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 2.3683 time to fit residues: 211.9988 Evaluate side-chains 82 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3396 Z= 0.270 Angle : 0.588 4.535 4548 Z= 0.312 Chirality : 0.050 0.120 516 Planarity : 0.004 0.029 576 Dihedral : 6.433 18.770 444 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.86 % Allowed : 19.01 % Favored : 78.12 % 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: -2.40 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE E 346 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.610 Fit side-chains REVERT: A 321 LYS cc_start: 0.7757 (tttt) cc_final: 0.7454 (mtpp) REVERT: A 338 GLU cc_start: 0.8081 (tt0) cc_final: 0.7320 (tm-30) REVERT: A 340 LYS cc_start: 0.8292 (mttt) cc_final: 0.7798 (mttt) REVERT: A 342 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6494 (pm20) REVERT: B 340 LYS cc_start: 0.8173 (mttt) cc_final: 0.7959 (mmtp) REVERT: B 369 LYS cc_start: 0.7911 (mttt) cc_final: 0.7410 (mttp) REVERT: C 311 LYS cc_start: 0.7196 (tttt) cc_final: 0.6607 (ttmt) REVERT: C 340 LYS cc_start: 0.7658 (mttt) cc_final: 0.7286 (mtmt) REVERT: C 342 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 311 LYS cc_start: 0.7543 (tttt) cc_final: 0.7110 (tttp) REVERT: D 321 LYS cc_start: 0.7210 (tttt) cc_final: 0.6660 (mtmt) REVERT: D 342 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: D 348 ASP cc_start: 0.7697 (t0) cc_final: 0.7360 (t0) REVERT: D 356 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7484 (t) REVERT: E 325 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8055 (tp) REVERT: E 353 LYS cc_start: 0.7427 (ttmt) cc_final: 0.7009 (ttpp) REVERT: E 356 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8302 (t) REVERT: F 315 LEU cc_start: 0.8097 (mp) cc_final: 0.7828 (mt) REVERT: F 345 ASP cc_start: 0.7294 (t0) cc_final: 0.6497 (m-30) REVERT: F 351 GLN cc_start: 0.7348 (mt0) cc_final: 0.7114 (mt0) REVERT: F 353 LYS cc_start: 0.7131 (mttt) cc_final: 0.6808 (mtpt) REVERT: F 356 SER cc_start: 0.8482 (p) cc_final: 0.8185 (p) REVERT: F 369 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7194 (mttm) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 2.7383 time to fit residues: 225.7397 Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3396 Z= 0.189 Angle : 0.544 4.107 4548 Z= 0.285 Chirality : 0.049 0.125 516 Planarity : 0.003 0.029 576 Dihedral : 6.130 18.553 444 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.65 % Allowed : 19.01 % Favored : 77.34 % 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: -2.40 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.007 0.001 PHE E 346 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.576 Fit side-chains REVERT: A 321 LYS cc_start: 0.7669 (tttt) cc_final: 0.7397 (mtpp) REVERT: A 338 GLU cc_start: 0.8041 (tt0) cc_final: 0.7285 (tm-30) REVERT: A 340 LYS cc_start: 0.8209 (mttt) cc_final: 0.7730 (mttt) REVERT: B 340 LYS cc_start: 0.8188 (mttt) cc_final: 0.7961 (mmtp) REVERT: B 369 LYS cc_start: 0.7889 (mttt) cc_final: 0.7361 (mttp) REVERT: C 311 LYS cc_start: 0.7196 (tttt) cc_final: 0.6579 (ttmt) REVERT: C 340 LYS cc_start: 0.7665 (mttt) cc_final: 0.7285 (mtmt) REVERT: C 342 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 311 LYS cc_start: 0.7514 (tttt) cc_final: 0.7063 (tttp) REVERT: D 321 LYS cc_start: 0.7297 (tttt) cc_final: 0.6674 (mtmt) REVERT: D 353 LYS cc_start: 0.7357 (mttt) cc_final: 0.6854 (mttt) REVERT: E 325 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (tp) REVERT: E 353 LYS cc_start: 0.7401 (ttmt) cc_final: 0.7006 (ttpp) REVERT: E 356 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8246 (t) REVERT: F 315 LEU cc_start: 0.8103 (mp) cc_final: 0.7850 (mt) REVERT: F 351 GLN cc_start: 0.7378 (mt0) cc_final: 0.7147 (mt0) REVERT: F 353 LYS cc_start: 0.7118 (mttt) cc_final: 0.6711 (mtpt) REVERT: F 356 SER cc_start: 0.8312 (p) cc_final: 0.8018 (p) REVERT: F 369 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7228 (mttm) outliers start: 14 outliers final: 7 residues processed: 81 average time/residue: 2.3020 time to fit residues: 192.1456 Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3396 Z= 0.286 Angle : 0.594 4.831 4548 Z= 0.314 Chirality : 0.050 0.121 516 Planarity : 0.004 0.028 576 Dihedral : 6.317 18.637 444 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.12 % Allowed : 19.53 % Favored : 77.34 % 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: -2.56 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE E 346 TYR 0.021 0.004 TYR D 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.574 Fit side-chains REVERT: A 321 LYS cc_start: 0.7777 (tttt) cc_final: 0.7461 (mtpp) REVERT: A 338 GLU cc_start: 0.8037 (tt0) cc_final: 0.7607 (tt0) REVERT: A 340 LYS cc_start: 0.8205 (mttt) cc_final: 0.7987 (mttt) REVERT: A 342 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6465 (pm20) REVERT: A 369 LYS cc_start: 0.7751 (mttt) cc_final: 0.7267 (mttp) REVERT: B 340 LYS cc_start: 0.8236 (mttt) cc_final: 0.7919 (mmmm) REVERT: B 369 LYS cc_start: 0.7951 (mttt) cc_final: 0.7355 (mttp) REVERT: C 311 LYS cc_start: 0.7313 (tttt) cc_final: 0.6666 (ttmt) REVERT: C 340 LYS cc_start: 0.7760 (mttt) cc_final: 0.7457 (mtmt) REVERT: C 342 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7327 (mm-30) REVERT: D 311 LYS cc_start: 0.7498 (tttt) cc_final: 0.7060 (tttp) REVERT: D 321 LYS cc_start: 0.7291 (tttt) cc_final: 0.6665 (mtmt) REVERT: D 342 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7193 (mp0) REVERT: D 348 ASP cc_start: 0.7731 (t0) cc_final: 0.7373 (t0) REVERT: D 353 LYS cc_start: 0.7365 (mttt) cc_final: 0.6868 (mttt) REVERT: E 343 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7139 (mmmt) REVERT: E 353 LYS cc_start: 0.7385 (ttmt) cc_final: 0.6974 (ttpp) REVERT: E 356 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8257 (t) REVERT: E 358 ASP cc_start: 0.7443 (m-30) cc_final: 0.7161 (m-30) REVERT: F 315 LEU cc_start: 0.8102 (mp) cc_final: 0.7863 (mt) REVERT: F 347 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7256 (mtmt) REVERT: F 351 GLN cc_start: 0.7381 (mt0) cc_final: 0.7101 (mt0) REVERT: F 356 SER cc_start: 0.8482 (p) cc_final: 0.8264 (p) REVERT: F 369 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7247 (mttm) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 2.4105 time to fit residues: 190.8323 Evaluate side-chains 76 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3396 Z= 0.153 Angle : 0.526 4.761 4548 Z= 0.272 Chirality : 0.049 0.124 516 Planarity : 0.003 0.030 576 Dihedral : 5.901 18.123 444 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.34 % Allowed : 20.31 % Favored : 77.34 % 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 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.004 0.001 PHE A 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.553 Fit side-chains REVERT: A 321 LYS cc_start: 0.7624 (tttt) cc_final: 0.7370 (mtpp) REVERT: A 338 GLU cc_start: 0.8016 (tt0) cc_final: 0.7298 (tm-30) REVERT: A 340 LYS cc_start: 0.8219 (mttt) cc_final: 0.7702 (mttt) REVERT: B 340 LYS cc_start: 0.8176 (mttt) cc_final: 0.7861 (mmmm) REVERT: B 342 GLU cc_start: 0.8029 (mm-30) cc_final: 0.5867 (mp0) REVERT: B 369 LYS cc_start: 0.7965 (mttt) cc_final: 0.7340 (mttp) REVERT: C 340 LYS cc_start: 0.7824 (mttt) cc_final: 0.7465 (mtmt) REVERT: C 342 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7355 (mm-30) REVERT: D 311 LYS cc_start: 0.7428 (tttt) cc_final: 0.7009 (tttp) REVERT: D 321 LYS cc_start: 0.7297 (tttt) cc_final: 0.6680 (mtmt) REVERT: D 353 LYS cc_start: 0.7332 (mttt) cc_final: 0.6843 (mttt) REVERT: E 342 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6734 (mm-30) REVERT: E 343 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7112 (mmmt) REVERT: E 353 LYS cc_start: 0.7381 (ttmt) cc_final: 0.6837 (ttpp) REVERT: F 315 LEU cc_start: 0.8132 (mp) cc_final: 0.7889 (mt) REVERT: F 351 GLN cc_start: 0.7338 (mt0) cc_final: 0.7061 (mt0) REVERT: F 356 SER cc_start: 0.8300 (p) cc_final: 0.7955 (p) outliers start: 9 outliers final: 9 residues processed: 74 average time/residue: 2.1696 time to fit residues: 165.7345 Evaluate side-chains 74 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3396 Z= 0.173 Angle : 0.527 3.935 4548 Z= 0.276 Chirality : 0.049 0.123 516 Planarity : 0.004 0.032 576 Dihedral : 5.806 17.494 444 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.08 % Allowed : 21.35 % Favored : 76.56 % 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: -2.39 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.006 0.001 PHE E 346 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.595 Fit side-chains REVERT: A 321 LYS cc_start: 0.7639 (tttt) cc_final: 0.7356 (mtpp) REVERT: A 338 GLU cc_start: 0.7977 (tt0) cc_final: 0.7268 (tm-30) REVERT: A 340 LYS cc_start: 0.8172 (mttt) cc_final: 0.7817 (mttt) REVERT: A 342 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6457 (pm20) REVERT: B 340 LYS cc_start: 0.8165 (mttt) cc_final: 0.7908 (mmmm) REVERT: B 342 GLU cc_start: 0.8041 (mm-30) cc_final: 0.5935 (mp0) REVERT: B 369 LYS cc_start: 0.7979 (mttt) cc_final: 0.7357 (mttp) REVERT: C 340 LYS cc_start: 0.7814 (mttt) cc_final: 0.7453 (mtmt) REVERT: C 342 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 311 LYS cc_start: 0.7419 (tttt) cc_final: 0.7007 (tttp) REVERT: D 321 LYS cc_start: 0.7292 (tttt) cc_final: 0.6675 (mtmt) REVERT: D 342 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7300 (mp0) REVERT: D 353 LYS cc_start: 0.7331 (mttt) cc_final: 0.6841 (mttt) REVERT: E 342 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6741 (mm-30) REVERT: E 343 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7113 (mmmt) REVERT: E 353 LYS cc_start: 0.7384 (ttmt) cc_final: 0.6979 (ttpp) REVERT: E 356 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (t) REVERT: F 315 LEU cc_start: 0.8116 (mp) cc_final: 0.7878 (mt) REVERT: F 351 GLN cc_start: 0.7319 (mt0) cc_final: 0.7041 (mt0) REVERT: F 353 LYS cc_start: 0.7088 (mttt) cc_final: 0.6690 (mtpt) REVERT: F 356 SER cc_start: 0.8396 (p) cc_final: 0.8108 (p) REVERT: F 369 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7217 (mttm) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 2.4681 time to fit residues: 182.9251 Evaluate side-chains 72 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3396 Z= 0.136 Angle : 0.505 4.105 4548 Z= 0.261 Chirality : 0.049 0.126 516 Planarity : 0.003 0.033 576 Dihedral : 5.579 16.844 444 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.04 % Allowed : 22.14 % Favored : 76.82 % 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: -2.31 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.003 0.001 PHE A 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.696 Fit side-chains REVERT: A 321 LYS cc_start: 0.7620 (tttt) cc_final: 0.7363 (mtpp) REVERT: A 338 GLU cc_start: 0.7954 (tt0) cc_final: 0.7255 (tm-30) REVERT: A 340 LYS cc_start: 0.8189 (mttt) cc_final: 0.7836 (mttt) REVERT: A 342 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6446 (pm20) REVERT: B 340 LYS cc_start: 0.8150 (mttt) cc_final: 0.7849 (mmmm) REVERT: B 342 GLU cc_start: 0.8091 (mm-30) cc_final: 0.5962 (mp0) REVERT: B 369 LYS cc_start: 0.7939 (mttt) cc_final: 0.7297 (mttp) REVERT: C 311 LYS cc_start: 0.7312 (tttt) cc_final: 0.6611 (ttmt) REVERT: C 340 LYS cc_start: 0.7826 (mttt) cc_final: 0.7463 (mtmt) REVERT: C 342 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7381 (mm-30) REVERT: D 311 LYS cc_start: 0.7362 (tttt) cc_final: 0.6964 (tttp) REVERT: D 321 LYS cc_start: 0.7303 (tttt) cc_final: 0.6679 (mtmt) REVERT: D 353 LYS cc_start: 0.7289 (mttt) cc_final: 0.6785 (mttt) REVERT: E 343 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7094 (mmmt) REVERT: E 353 LYS cc_start: 0.7400 (ttmt) cc_final: 0.6862 (ttpp) REVERT: F 315 LEU cc_start: 0.8083 (mp) cc_final: 0.7851 (mt) REVERT: F 343 LYS cc_start: 0.8004 (mptt) cc_final: 0.7627 (mtpp) REVERT: F 351 GLN cc_start: 0.7223 (mt0) cc_final: 0.6982 (mt0) REVERT: F 353 LYS cc_start: 0.7143 (mttt) cc_final: 0.6789 (mtpt) REVERT: F 356 SER cc_start: 0.8349 (p) cc_final: 0.8000 (p) REVERT: F 369 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7012 (ptpt) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 2.7219 time to fit residues: 218.3307 Evaluate side-chains 72 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.174896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.143837 restraints weight = 9900.957| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.76 r_work: 0.4043 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.178 Angle : 0.531 3.919 4548 Z= 0.277 Chirality : 0.049 0.124 516 Planarity : 0.004 0.032 576 Dihedral : 5.616 16.830 444 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.30 % Allowed : 22.92 % Favored : 75.78 % 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: -2.35 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.006 0.001 PHE E 346 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4955.44 seconds wall clock time: 86 minutes 18.92 seconds (5178.92 seconds total)