Starting phenix.real_space_refine on Tue Sep 24 05:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/09_2024/8q2k_18111.cif" } resolution = 2.88 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= 0.004 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.40, per 1000 atoms: 0.63 Number of scatterers: 7032 At special positions: 0 Unit cell: (132.314, 111.958, 41.439, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 1.64 Conformation dependent library (CDL) restraints added in 549.1 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.525A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.849A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.474A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.690A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.529A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.382A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.399A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.427A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.654A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.561A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.884A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.512A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.664A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.404A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.606A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.477A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.756A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 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: 2.29 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.46: 1059 1.46 - 1.64: 1869 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N ARG D 349 " pdb=" H ARG D 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 HIS F 374 " pdb=" HE1 HIS F 374 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLU B 372 " pdb=" H GLU B 372 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS F 362 " pdb=" HD2 HIS F 362 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" ND1 HIS C 362 " pdb=" HD1 HIS C 362 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11064 2.63 - 5.27: 1456 5.27 - 7.90: 377 7.90 - 10.54: 9 10.54 - 13.17: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.61 6.59 1.30e+00 5.92e-01 2.57e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.64 6.56 1.30e+00 5.92e-01 2.55e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta sigma weight residual 122.37 129.17 -6.80 1.54e+00 4.22e-01 1.95e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 2914 15.15 - 30.31: 169 30.31 - 45.46: 69 45.46 - 60.61: 66 60.61 - 75.76: 46 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA GLN A 307 " pdb=" C GLN A 307 " pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" C LYS F 343 " pdb=" N LYS F 343 " pdb=" CA LYS F 343 " pdb=" CB LYS F 343 " ideal model delta harmonic sigma weight residual -122.60 -130.95 8.35 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA THR F 319 " pdb=" C THR F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 242 0.050 - 0.099: 214 0.099 - 0.148: 57 0.148 - 0.197: 12 0.197 - 0.246: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LYS E 331 " pdb=" N LYS E 331 " pdb=" C LYS E 331 " pdb=" CB LYS E 331 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 374 " -0.095 2.00e-02 2.50e+03 5.49e-02 6.77e+01 pdb=" CG HIS D 374 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS D 374 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS D 374 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS D 374 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS D 374 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS D 374 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS D 374 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 HIS D 374 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.086 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.089 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS C 374 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.085 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 603 2.18 - 2.79: 12295 2.79 - 3.39: 18077 3.39 - 4.00: 25062 4.00 - 4.60: 34061 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.588 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.591 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.627 2.450 ... (remaining 90093 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: 3.360 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.034 3498 Z= 0.750 Angle : 1.799 6.798 4680 Z= 1.181 Chirality : 0.070 0.246 528 Planarity : 0.009 0.040 594 Dihedral : 10.493 67.213 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.81 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS B 362 PHE 0.057 0.020 PHE C 346 TYR 0.046 0.009 TYR E 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6833 (tt0) cc_final: 0.6071 (tp30) REVERT: A 345 ASP cc_start: 0.7509 (t0) cc_final: 0.7099 (m-30) REVERT: A 353 LYS cc_start: 0.6953 (mttt) cc_final: 0.6643 (tmtp) REVERT: A 369 LYS cc_start: 0.6927 (tttt) cc_final: 0.6665 (ttpt) REVERT: B 336 GLN cc_start: 0.8112 (tt0) cc_final: 0.7902 (tt0) REVERT: B 338 GLU cc_start: 0.7620 (tt0) cc_final: 0.7357 (tt0) REVERT: B 340 LYS cc_start: 0.7237 (tttt) cc_final: 0.6328 (tmtm) REVERT: B 342 GLU cc_start: 0.7244 (tt0) cc_final: 0.6922 (tt0) REVERT: B 353 LYS cc_start: 0.6929 (mttt) cc_final: 0.6693 (tttm) REVERT: C 317 LYS cc_start: 0.7883 (mttt) cc_final: 0.7527 (mtpt) REVERT: C 338 GLU cc_start: 0.7478 (tt0) cc_final: 0.6733 (tp30) REVERT: C 353 LYS cc_start: 0.7589 (mttt) cc_final: 0.7178 (tmtp) REVERT: D 331 LYS cc_start: 0.7713 (mttt) cc_final: 0.7218 (mmmt) REVERT: D 336 GLN cc_start: 0.8535 (tt0) cc_final: 0.8326 (tt0) REVERT: D 340 LYS cc_start: 0.8070 (tttt) cc_final: 0.7304 (tptt) REVERT: D 342 GLU cc_start: 0.7679 (tt0) cc_final: 0.7387 (tt0) REVERT: D 347 LYS cc_start: 0.7856 (mttt) cc_final: 0.7486 (mmtm) REVERT: D 349 ARG cc_start: 0.6417 (mtm180) cc_final: 0.4258 (pmt-80) REVERT: D 353 LYS cc_start: 0.7654 (mttt) cc_final: 0.7375 (tttm) REVERT: D 358 ASP cc_start: 0.7846 (m-30) cc_final: 0.7598 (m-30) REVERT: E 311 LYS cc_start: 0.6760 (mttt) cc_final: 0.5686 (mmtt) REVERT: E 338 GLU cc_start: 0.6683 (tt0) cc_final: 0.6004 (tp30) REVERT: E 345 ASP cc_start: 0.7525 (t0) cc_final: 0.7205 (m-30) REVERT: E 353 LYS cc_start: 0.6974 (mttt) cc_final: 0.6665 (tttm) REVERT: E 369 LYS cc_start: 0.7106 (tttt) cc_final: 0.6523 (ttmp) REVERT: F 311 LYS cc_start: 0.7287 (mttt) cc_final: 0.6020 (mmtt) REVERT: F 338 GLU cc_start: 0.7409 (tt0) cc_final: 0.7026 (tm-30) REVERT: F 340 LYS cc_start: 0.7381 (tttt) cc_final: 0.6549 (tptt) REVERT: F 349 ARG cc_start: 0.5764 (mtm180) cc_final: 0.5079 (mmp80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 3.6750 time to fit residues: 464.1749 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3498 Z= 0.372 Angle : 0.587 4.710 4680 Z= 0.314 Chirality : 0.050 0.131 528 Planarity : 0.005 0.039 594 Dihedral : 5.582 13.277 462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.26 % Allowed : 11.62 % Favored : 87.12 % 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: -1.77 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 329 PHE 0.011 0.003 PHE E 346 TYR 0.006 0.001 TYR C 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7009 (tt0) cc_final: 0.6185 (tp30) REVERT: A 345 ASP cc_start: 0.7611 (t0) cc_final: 0.7314 (m-30) REVERT: A 347 LYS cc_start: 0.8085 (mttt) cc_final: 0.7857 (mptp) REVERT: A 353 LYS cc_start: 0.6887 (mttt) cc_final: 0.6649 (tmtp) REVERT: A 369 LYS cc_start: 0.7142 (tttt) cc_final: 0.6538 (ttmp) REVERT: B 336 GLN cc_start: 0.8114 (tt0) cc_final: 0.7878 (tt0) REVERT: B 340 LYS cc_start: 0.7255 (tttt) cc_final: 0.6349 (tmtm) REVERT: B 342 GLU cc_start: 0.7090 (tt0) cc_final: 0.6822 (tt0) REVERT: B 353 LYS cc_start: 0.6955 (mttt) cc_final: 0.6735 (tttm) REVERT: C 317 LYS cc_start: 0.7835 (mttt) cc_final: 0.7384 (mtpt) REVERT: C 338 GLU cc_start: 0.7432 (tt0) cc_final: 0.6685 (tp30) REVERT: C 340 LYS cc_start: 0.7747 (tttt) cc_final: 0.7415 (ttpp) REVERT: C 349 ARG cc_start: 0.6441 (mtm-85) cc_final: 0.4813 (mtt90) REVERT: C 351 GLN cc_start: 0.8185 (tt0) cc_final: 0.7798 (tt0) REVERT: C 353 LYS cc_start: 0.7479 (mttt) cc_final: 0.7098 (tmtp) REVERT: D 340 LYS cc_start: 0.7973 (tttt) cc_final: 0.7184 (tptt) REVERT: D 342 GLU cc_start: 0.7590 (tt0) cc_final: 0.7343 (tt0) REVERT: D 347 LYS cc_start: 0.7992 (mttt) cc_final: 0.7698 (mmtm) REVERT: D 349 ARG cc_start: 0.6735 (mtm180) cc_final: 0.4407 (pmt-80) REVERT: D 353 LYS cc_start: 0.7611 (mttt) cc_final: 0.7358 (tttm) REVERT: E 311 LYS cc_start: 0.6926 (mttt) cc_final: 0.5760 (mmtt) REVERT: E 338 GLU cc_start: 0.6763 (tt0) cc_final: 0.6052 (tp30) REVERT: E 340 LYS cc_start: 0.7205 (tttt) cc_final: 0.6857 (ttpp) REVERT: E 345 ASP cc_start: 0.7590 (t0) cc_final: 0.7267 (m-30) REVERT: E 353 LYS cc_start: 0.7098 (mttt) cc_final: 0.6805 (tmtp) REVERT: E 369 LYS cc_start: 0.7223 (tttt) cc_final: 0.6642 (ttmp) REVERT: F 340 LYS cc_start: 0.7319 (tttt) cc_final: 0.6465 (tptt) REVERT: F 349 ARG cc_start: 0.6008 (mtm180) cc_final: 0.5054 (mmp80) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 3.6654 time to fit residues: 328.6136 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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: 3.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.166 Angle : 0.481 4.330 4680 Z= 0.246 Chirality : 0.050 0.134 528 Planarity : 0.004 0.030 594 Dihedral : 4.789 11.970 462 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 13.89 % Favored : 85.10 % 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: -1.67 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE C 378 TYR 0.006 0.001 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6376 (mt) cc_final: 0.6034 (mp) REVERT: A 338 GLU cc_start: 0.7023 (tt0) cc_final: 0.6239 (tp30) REVERT: A 345 ASP cc_start: 0.7675 (t0) cc_final: 0.7336 (m-30) REVERT: A 347 LYS cc_start: 0.8086 (mttt) cc_final: 0.7842 (mptp) REVERT: A 351 GLN cc_start: 0.7572 (tt0) cc_final: 0.7105 (tt0) REVERT: A 353 LYS cc_start: 0.6890 (mttt) cc_final: 0.6644 (tmtp) REVERT: A 369 LYS cc_start: 0.7195 (tttt) cc_final: 0.6960 (ttpt) REVERT: B 336 GLN cc_start: 0.8088 (tt0) cc_final: 0.7867 (tt0) REVERT: B 340 LYS cc_start: 0.7201 (tttt) cc_final: 0.6334 (tmtm) REVERT: B 342 GLU cc_start: 0.7085 (tt0) cc_final: 0.6859 (tt0) REVERT: C 338 GLU cc_start: 0.7328 (tt0) cc_final: 0.6642 (tp30) REVERT: C 340 LYS cc_start: 0.7754 (tttt) cc_final: 0.7444 (ttpp) REVERT: C 349 ARG cc_start: 0.6170 (mtm-85) cc_final: 0.4778 (mtt90) REVERT: C 353 LYS cc_start: 0.7435 (mttt) cc_final: 0.7064 (tmtp) REVERT: D 340 LYS cc_start: 0.7927 (tttt) cc_final: 0.7173 (tptt) REVERT: D 342 GLU cc_start: 0.7563 (tt0) cc_final: 0.7335 (tt0) REVERT: D 347 LYS cc_start: 0.7970 (mttt) cc_final: 0.7683 (mmtm) REVERT: D 353 LYS cc_start: 0.7669 (mttt) cc_final: 0.7397 (tttm) REVERT: E 338 GLU cc_start: 0.6784 (tt0) cc_final: 0.6113 (tp30) REVERT: E 340 LYS cc_start: 0.7132 (tttt) cc_final: 0.6811 (ttpp) REVERT: E 345 ASP cc_start: 0.7594 (t0) cc_final: 0.7226 (m-30) REVERT: E 353 LYS cc_start: 0.7102 (mttt) cc_final: 0.6860 (tmtp) REVERT: E 369 LYS cc_start: 0.7203 (tttt) cc_final: 0.6634 (ttmp) REVERT: F 340 LYS cc_start: 0.7279 (tttt) cc_final: 0.6427 (tptt) REVERT: F 349 ARG cc_start: 0.6113 (mtm180) cc_final: 0.5087 (mmp80) REVERT: F 372 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7061 (tt0) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 3.6417 time to fit residues: 286.0535 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.153 Angle : 0.454 4.160 4680 Z= 0.229 Chirality : 0.050 0.126 528 Planarity : 0.003 0.023 594 Dihedral : 4.427 11.592 462 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 15.66 % Favored : 82.83 % 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: -1.51 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.005 0.001 PHE E 346 TYR 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6342 (mt) cc_final: 0.6032 (mp) REVERT: A 338 GLU cc_start: 0.7028 (tt0) cc_final: 0.6183 (tp30) REVERT: A 345 ASP cc_start: 0.7653 (t0) cc_final: 0.7327 (m-30) REVERT: A 351 GLN cc_start: 0.7591 (tt0) cc_final: 0.7131 (tt0) REVERT: A 353 LYS cc_start: 0.6873 (mttt) cc_final: 0.6607 (tmtp) REVERT: A 369 LYS cc_start: 0.7231 (tttt) cc_final: 0.6983 (ttpt) REVERT: B 336 GLN cc_start: 0.8089 (tt0) cc_final: 0.7865 (tt0) REVERT: B 340 LYS cc_start: 0.7183 (tttt) cc_final: 0.6326 (tmtm) REVERT: B 342 GLU cc_start: 0.7099 (tt0) cc_final: 0.6884 (tt0) REVERT: C 338 GLU cc_start: 0.7308 (tt0) cc_final: 0.6600 (tp30) REVERT: C 340 LYS cc_start: 0.7767 (tttt) cc_final: 0.7470 (ttpp) REVERT: C 347 LYS cc_start: 0.8608 (mppt) cc_final: 0.8206 (mptp) REVERT: C 353 LYS cc_start: 0.7501 (mttt) cc_final: 0.7087 (tmtp) REVERT: D 340 LYS cc_start: 0.7918 (tttt) cc_final: 0.7171 (tptt) REVERT: D 342 GLU cc_start: 0.7536 (tt0) cc_final: 0.7313 (tt0) REVERT: D 347 LYS cc_start: 0.7952 (mttt) cc_final: 0.7681 (mmtm) REVERT: D 353 LYS cc_start: 0.7685 (mttt) cc_final: 0.7390 (tttm) REVERT: E 317 LYS cc_start: 0.7504 (mttt) cc_final: 0.6521 (tttp) REVERT: E 338 GLU cc_start: 0.6789 (tt0) cc_final: 0.6074 (tp30) REVERT: E 340 LYS cc_start: 0.7080 (tttt) cc_final: 0.6773 (ttpp) REVERT: E 345 ASP cc_start: 0.7662 (t0) cc_final: 0.7250 (m-30) REVERT: E 351 GLN cc_start: 0.7654 (tt0) cc_final: 0.7147 (tt0) REVERT: E 353 LYS cc_start: 0.7150 (mttt) cc_final: 0.6850 (tmtp) REVERT: E 369 LYS cc_start: 0.7185 (tttt) cc_final: 0.6619 (ttmp) REVERT: F 340 LYS cc_start: 0.7219 (tttt) cc_final: 0.6379 (tptt) REVERT: F 349 ARG cc_start: 0.6152 (mtm180) cc_final: 0.5069 (mmp80) outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 3.3903 time to fit residues: 276.9208 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.129 Angle : 0.439 4.099 4680 Z= 0.221 Chirality : 0.050 0.127 528 Planarity : 0.003 0.021 594 Dihedral : 4.212 11.205 462 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % 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: -1.43 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.004 0.001 PHE A 378 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6342 (mt) cc_final: 0.6048 (mp) REVERT: A 338 GLU cc_start: 0.7027 (tt0) cc_final: 0.6224 (tp30) REVERT: A 345 ASP cc_start: 0.7640 (t0) cc_final: 0.7302 (m-30) REVERT: A 351 GLN cc_start: 0.7575 (tt0) cc_final: 0.7181 (tt0) REVERT: A 353 LYS cc_start: 0.6867 (mttt) cc_final: 0.6629 (tmtp) REVERT: B 336 GLN cc_start: 0.8099 (tt0) cc_final: 0.7876 (tt0) REVERT: B 340 LYS cc_start: 0.7191 (tttt) cc_final: 0.6345 (tmtm) REVERT: B 342 GLU cc_start: 0.7101 (tt0) cc_final: 0.6898 (tt0) REVERT: B 353 LYS cc_start: 0.6924 (mttt) cc_final: 0.6720 (tttm) REVERT: C 338 GLU cc_start: 0.7301 (tt0) cc_final: 0.6606 (tp30) REVERT: C 340 LYS cc_start: 0.7774 (tttt) cc_final: 0.7459 (ttpp) REVERT: C 347 LYS cc_start: 0.8627 (mppt) cc_final: 0.8244 (mptp) REVERT: C 353 LYS cc_start: 0.7481 (mttt) cc_final: 0.7069 (tmtp) REVERT: D 317 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7919 (mttm) REVERT: D 340 LYS cc_start: 0.7918 (tttt) cc_final: 0.7178 (tptt) REVERT: D 342 GLU cc_start: 0.7568 (tt0) cc_final: 0.7350 (tt0) REVERT: D 347 LYS cc_start: 0.8000 (mttt) cc_final: 0.7725 (mmtm) REVERT: D 351 GLN cc_start: 0.7819 (tt0) cc_final: 0.7611 (mt0) REVERT: D 353 LYS cc_start: 0.7597 (mttt) cc_final: 0.7338 (tttm) REVERT: E 317 LYS cc_start: 0.7470 (mttt) cc_final: 0.6512 (tttp) REVERT: E 338 GLU cc_start: 0.6737 (tt0) cc_final: 0.6095 (tp30) REVERT: E 340 LYS cc_start: 0.7014 (tttt) cc_final: 0.6738 (ttpp) REVERT: E 345 ASP cc_start: 0.7686 (t0) cc_final: 0.7245 (m-30) REVERT: E 351 GLN cc_start: 0.7681 (tt0) cc_final: 0.7143 (tt0) REVERT: E 353 LYS cc_start: 0.7195 (mttt) cc_final: 0.6846 (tmtp) REVERT: E 369 LYS cc_start: 0.7180 (tttt) cc_final: 0.6606 (ttmp) REVERT: F 340 LYS cc_start: 0.7214 (tttt) cc_final: 0.6370 (tptt) REVERT: F 349 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5065 (mmp80) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 3.2906 time to fit residues: 258.9757 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.099 Angle : 0.421 3.975 4680 Z= 0.209 Chirality : 0.051 0.124 528 Planarity : 0.002 0.020 594 Dihedral : 3.836 10.110 462 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 17.42 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 330 PHE 0.002 0.001 PHE E 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6306 (mt) cc_final: 0.6036 (mp) REVERT: A 338 GLU cc_start: 0.7047 (tt0) cc_final: 0.6211 (tp30) REVERT: A 345 ASP cc_start: 0.7603 (t0) cc_final: 0.7248 (m-30) REVERT: A 351 GLN cc_start: 0.7443 (tt0) cc_final: 0.7087 (tt0) REVERT: A 353 LYS cc_start: 0.6953 (mttt) cc_final: 0.6588 (tmtp) REVERT: B 338 GLU cc_start: 0.7525 (tt0) cc_final: 0.7038 (tm-30) REVERT: B 340 LYS cc_start: 0.7114 (tttt) cc_final: 0.6325 (tmtm) REVERT: B 342 GLU cc_start: 0.7079 (tt0) cc_final: 0.6852 (tt0) REVERT: B 351 GLN cc_start: 0.7100 (tt0) cc_final: 0.6893 (mt0) REVERT: C 338 GLU cc_start: 0.7259 (tt0) cc_final: 0.6578 (tp30) REVERT: C 340 LYS cc_start: 0.7737 (tttt) cc_final: 0.7440 (ttpp) REVERT: C 347 LYS cc_start: 0.8623 (mppt) cc_final: 0.8227 (mptp) REVERT: C 353 LYS cc_start: 0.7538 (mttt) cc_final: 0.7063 (tmtp) REVERT: D 317 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7971 (mttm) REVERT: D 340 LYS cc_start: 0.7925 (tttt) cc_final: 0.7161 (tptt) REVERT: D 342 GLU cc_start: 0.7556 (tt0) cc_final: 0.7327 (tt0) REVERT: D 347 LYS cc_start: 0.7945 (mttt) cc_final: 0.7694 (mmtm) REVERT: D 353 LYS cc_start: 0.7507 (mttt) cc_final: 0.7287 (tttm) REVERT: E 317 LYS cc_start: 0.7519 (mttt) cc_final: 0.6545 (tttp) REVERT: E 338 GLU cc_start: 0.6779 (tt0) cc_final: 0.6076 (tp30) REVERT: E 340 LYS cc_start: 0.6926 (tttt) cc_final: 0.6669 (ttpp) REVERT: E 345 ASP cc_start: 0.7667 (t0) cc_final: 0.7236 (m-30) REVERT: E 351 GLN cc_start: 0.7679 (tt0) cc_final: 0.7167 (tt0) REVERT: E 353 LYS cc_start: 0.7209 (mttt) cc_final: 0.6872 (tmtp) REVERT: E 369 LYS cc_start: 0.7260 (tttt) cc_final: 0.6698 (ttmp) REVERT: F 340 LYS cc_start: 0.7142 (tttt) cc_final: 0.6283 (tptt) REVERT: F 349 ARG cc_start: 0.6235 (mtm180) cc_final: 0.5130 (mmp80) REVERT: F 351 GLN cc_start: 0.7381 (tt0) cc_final: 0.7109 (tt0) outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 3.1708 time to fit residues: 278.9427 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.169 Angle : 0.449 4.096 4680 Z= 0.225 Chirality : 0.050 0.126 528 Planarity : 0.003 0.023 594 Dihedral : 4.089 11.620 462 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.26 % Allowed : 18.94 % Favored : 79.80 % 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: -1.50 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.007 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6353 (mt) cc_final: 0.6054 (mp) REVERT: A 338 GLU cc_start: 0.6987 (tt0) cc_final: 0.6208 (tp30) REVERT: A 345 ASP cc_start: 0.7673 (t0) cc_final: 0.7289 (m-30) REVERT: A 351 GLN cc_start: 0.7483 (tt0) cc_final: 0.7095 (tt0) REVERT: A 353 LYS cc_start: 0.7004 (mttt) cc_final: 0.6630 (tmtp) REVERT: B 340 LYS cc_start: 0.7190 (tttt) cc_final: 0.6342 (tmtm) REVERT: B 342 GLU cc_start: 0.7118 (tt0) cc_final: 0.6895 (tt0) REVERT: C 338 GLU cc_start: 0.7308 (tt0) cc_final: 0.6604 (tp30) REVERT: C 340 LYS cc_start: 0.7788 (tttt) cc_final: 0.7483 (ttpp) REVERT: C 347 LYS cc_start: 0.8639 (mppt) cc_final: 0.8244 (mptp) REVERT: C 353 LYS cc_start: 0.7543 (mttt) cc_final: 0.7110 (tmtp) REVERT: D 317 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7969 (mttm) REVERT: D 340 LYS cc_start: 0.7933 (tttt) cc_final: 0.7170 (tptt) REVERT: D 342 GLU cc_start: 0.7545 (tt0) cc_final: 0.7283 (tt0) REVERT: D 347 LYS cc_start: 0.7994 (mttt) cc_final: 0.7710 (mmtm) REVERT: E 317 LYS cc_start: 0.7482 (mttt) cc_final: 0.6463 (ttmm) REVERT: E 338 GLU cc_start: 0.6764 (tt0) cc_final: 0.6103 (tp30) REVERT: E 340 LYS cc_start: 0.6997 (tttt) cc_final: 0.6728 (ttpp) REVERT: E 345 ASP cc_start: 0.7700 (t0) cc_final: 0.7215 (m-30) REVERT: E 351 GLN cc_start: 0.7638 (tt0) cc_final: 0.7198 (tt0) REVERT: E 353 LYS cc_start: 0.7157 (mttt) cc_final: 0.6799 (tmtp) REVERT: E 369 LYS cc_start: 0.7149 (tttt) cc_final: 0.6582 (ttmp) REVERT: F 340 LYS cc_start: 0.7201 (tttt) cc_final: 0.6364 (tptt) REVERT: F 349 ARG cc_start: 0.6213 (mtm180) cc_final: 0.5063 (mmp80) REVERT: F 351 GLN cc_start: 0.7403 (tt0) cc_final: 0.7173 (tt0) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 3.4742 time to fit residues: 248.4755 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.0000 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.127 Angle : 0.431 4.015 4680 Z= 0.215 Chirality : 0.050 0.124 528 Planarity : 0.003 0.024 594 Dihedral : 3.941 11.254 462 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 19.44 % Favored : 79.55 % 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: -1.48 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 330 PHE 0.004 0.001 PHE A 378 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6364 (mt) cc_final: 0.6077 (mp) REVERT: A 338 GLU cc_start: 0.6991 (tt0) cc_final: 0.6624 (tt0) REVERT: A 345 ASP cc_start: 0.7630 (t0) cc_final: 0.7289 (m-30) REVERT: A 351 GLN cc_start: 0.7466 (tt0) cc_final: 0.7095 (tt0) REVERT: A 353 LYS cc_start: 0.7002 (mttt) cc_final: 0.6645 (tmtp) REVERT: B 340 LYS cc_start: 0.7171 (tttt) cc_final: 0.6333 (tmtm) REVERT: B 342 GLU cc_start: 0.7115 (tt0) cc_final: 0.6900 (tt0) REVERT: C 338 GLU cc_start: 0.7276 (tt0) cc_final: 0.6567 (tp30) REVERT: C 340 LYS cc_start: 0.7783 (tttt) cc_final: 0.7482 (ttpp) REVERT: C 347 LYS cc_start: 0.8628 (mppt) cc_final: 0.8238 (mptp) REVERT: C 353 LYS cc_start: 0.7570 (mttt) cc_final: 0.7133 (tmtp) REVERT: D 317 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7998 (mttm) REVERT: D 340 LYS cc_start: 0.7930 (tttt) cc_final: 0.7170 (tptt) REVERT: D 342 GLU cc_start: 0.7539 (tt0) cc_final: 0.7285 (tt0) REVERT: D 347 LYS cc_start: 0.7946 (mttt) cc_final: 0.7691 (mmtm) REVERT: E 317 LYS cc_start: 0.7492 (mttt) cc_final: 0.6462 (tttp) REVERT: E 331 LYS cc_start: 0.8272 (mttt) cc_final: 0.8056 (mttt) REVERT: E 338 GLU cc_start: 0.6758 (tt0) cc_final: 0.6152 (tp30) REVERT: E 340 LYS cc_start: 0.6920 (tttt) cc_final: 0.6661 (ttpp) REVERT: E 345 ASP cc_start: 0.7707 (t0) cc_final: 0.7198 (m-30) REVERT: E 351 GLN cc_start: 0.7670 (tt0) cc_final: 0.7167 (tt0) REVERT: E 353 LYS cc_start: 0.7183 (mttt) cc_final: 0.6836 (tmtp) REVERT: E 369 LYS cc_start: 0.7208 (tttt) cc_final: 0.6643 (ttmp) REVERT: F 340 LYS cc_start: 0.7170 (tttt) cc_final: 0.6338 (tptt) REVERT: F 349 ARG cc_start: 0.6259 (mtm180) cc_final: 0.5082 (mmp80) REVERT: F 351 GLN cc_start: 0.7425 (tt0) cc_final: 0.7179 (tt0) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 3.2662 time to fit residues: 240.5537 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.199 Angle : 0.458 4.177 4680 Z= 0.231 Chirality : 0.050 0.126 528 Planarity : 0.003 0.026 594 Dihedral : 4.195 12.039 462 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.26 % Allowed : 19.70 % Favored : 79.04 % 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: -1.62 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.002 PHE A 378 TYR 0.005 0.001 TYR B 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.587 Fit side-chains REVERT: A 308 ILE cc_start: 0.6366 (mt) cc_final: 0.6054 (mp) REVERT: A 317 LYS cc_start: 0.7221 (mttt) cc_final: 0.6415 (mtpt) REVERT: A 338 GLU cc_start: 0.6992 (tt0) cc_final: 0.6209 (tp30) REVERT: A 340 LYS cc_start: 0.7205 (tttt) cc_final: 0.6845 (ttpp) REVERT: A 345 ASP cc_start: 0.7705 (t0) cc_final: 0.7316 (m-30) REVERT: A 351 GLN cc_start: 0.7539 (tt0) cc_final: 0.7170 (tt0) REVERT: A 353 LYS cc_start: 0.7017 (mttt) cc_final: 0.6644 (tmtp) REVERT: B 340 LYS cc_start: 0.7202 (tttt) cc_final: 0.6358 (tmtm) REVERT: B 342 GLU cc_start: 0.7126 (tt0) cc_final: 0.6922 (tt0) REVERT: C 317 LYS cc_start: 0.7847 (mttt) cc_final: 0.7095 (mtpt) REVERT: C 338 GLU cc_start: 0.7336 (tt0) cc_final: 0.6664 (tp30) REVERT: C 340 LYS cc_start: 0.7763 (tttt) cc_final: 0.7438 (ttpp) REVERT: C 347 LYS cc_start: 0.8632 (mppt) cc_final: 0.8220 (mptp) REVERT: C 349 ARG cc_start: 0.6393 (mtm-85) cc_final: 0.5035 (mtt90) REVERT: C 353 LYS cc_start: 0.7551 (mttt) cc_final: 0.7141 (tmtp) REVERT: D 317 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8025 (mttm) REVERT: D 340 LYS cc_start: 0.7944 (tttt) cc_final: 0.7173 (tptt) REVERT: D 342 GLU cc_start: 0.7558 (tt0) cc_final: 0.7303 (tt0) REVERT: D 347 LYS cc_start: 0.7955 (mttt) cc_final: 0.7683 (mmtm) REVERT: D 349 ARG cc_start: 0.6918 (mtm180) cc_final: 0.4342 (pmt-80) REVERT: E 317 LYS cc_start: 0.7473 (mttt) cc_final: 0.6392 (tttp) REVERT: E 338 GLU cc_start: 0.6782 (tt0) cc_final: 0.6086 (tp30) REVERT: E 340 LYS cc_start: 0.7035 (tttt) cc_final: 0.6738 (ttpp) REVERT: E 345 ASP cc_start: 0.7717 (t0) cc_final: 0.7210 (m-30) REVERT: E 351 GLN cc_start: 0.7633 (tt0) cc_final: 0.7173 (tt0) REVERT: E 353 LYS cc_start: 0.7115 (mttt) cc_final: 0.6787 (tmtp) REVERT: E 369 LYS cc_start: 0.7137 (tttt) cc_final: 0.6571 (ttmp) REVERT: F 340 LYS cc_start: 0.7211 (tttt) cc_final: 0.6364 (tptt) REVERT: F 349 ARG cc_start: 0.6269 (mtm180) cc_final: 0.5040 (mmp80) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 3.4220 time to fit residues: 262.1297 Evaluate side-chains 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.180 Angle : 0.449 4.171 4680 Z= 0.227 Chirality : 0.050 0.125 528 Planarity : 0.003 0.026 594 Dihedral : 4.149 12.062 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.26 % Allowed : 20.20 % Favored : 78.54 % 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: -1.71 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE A 378 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.600 Fit side-chains REVERT: A 308 ILE cc_start: 0.6412 (mt) cc_final: 0.6098 (mp) REVERT: A 317 LYS cc_start: 0.7198 (mttt) cc_final: 0.6408 (mtpt) REVERT: A 338 GLU cc_start: 0.6985 (tt0) cc_final: 0.6206 (tp30) REVERT: A 340 LYS cc_start: 0.7213 (tttt) cc_final: 0.6847 (ttpp) REVERT: A 345 ASP cc_start: 0.7657 (t0) cc_final: 0.7291 (m-30) REVERT: A 351 GLN cc_start: 0.7552 (tt0) cc_final: 0.7172 (tt0) REVERT: A 353 LYS cc_start: 0.7007 (mttt) cc_final: 0.6645 (tmtp) REVERT: B 340 LYS cc_start: 0.7195 (tttt) cc_final: 0.6353 (tmtm) REVERT: B 342 GLU cc_start: 0.7105 (tt0) cc_final: 0.6903 (tt0) REVERT: C 317 LYS cc_start: 0.7779 (mttt) cc_final: 0.7049 (mtpt) REVERT: C 338 GLU cc_start: 0.7330 (tt0) cc_final: 0.6654 (tp30) REVERT: C 340 LYS cc_start: 0.7772 (tttt) cc_final: 0.7441 (ttpp) REVERT: C 347 LYS cc_start: 0.8643 (mppt) cc_final: 0.8230 (mptp) REVERT: C 349 ARG cc_start: 0.6394 (mtm-85) cc_final: 0.5102 (mtt90) REVERT: C 353 LYS cc_start: 0.7540 (mttt) cc_final: 0.7151 (tmtp) REVERT: D 317 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8018 (mttm) REVERT: D 340 LYS cc_start: 0.7950 (tttt) cc_final: 0.7164 (tptt) REVERT: D 342 GLU cc_start: 0.7555 (tt0) cc_final: 0.7295 (tt0) REVERT: D 347 LYS cc_start: 0.7984 (mttt) cc_final: 0.7709 (mmtm) REVERT: E 317 LYS cc_start: 0.7481 (mttt) cc_final: 0.6412 (tttp) REVERT: E 338 GLU cc_start: 0.6766 (tt0) cc_final: 0.6079 (tp30) REVERT: E 340 LYS cc_start: 0.7013 (tttt) cc_final: 0.6723 (ttpp) REVERT: E 345 ASP cc_start: 0.7709 (t0) cc_final: 0.7187 (m-30) REVERT: E 351 GLN cc_start: 0.7633 (tt0) cc_final: 0.7175 (tt0) REVERT: E 353 LYS cc_start: 0.7139 (mttt) cc_final: 0.6818 (tmtp) REVERT: E 369 LYS cc_start: 0.7187 (tttt) cc_final: 0.6621 (ttmp) REVERT: F 340 LYS cc_start: 0.7176 (tttt) cc_final: 0.6349 (tptt) REVERT: F 349 ARG cc_start: 0.6306 (mtm180) cc_final: 0.5039 (mmp80) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 3.3342 time to fit residues: 245.2389 Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.144870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136818 restraints weight = 14632.620| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.37 r_work: 0.3895 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.101 Angle : 0.418 3.915 4680 Z= 0.207 Chirality : 0.051 0.122 528 Planarity : 0.003 0.024 594 Dihedral : 3.727 11.018 462 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 20.45 % Favored : 78.54 % 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: -1.54 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.003 0.000 PHE C 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5121.99 seconds wall clock time: 88 minutes 51.48 seconds (5331.48 seconds total)