Starting phenix.real_space_refine on Sun Mar 10 17:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hre_0259/03_2024/6hre_0259.pdb" } resolution = 3.2 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= 0.007 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.29, per 1000 atoms: 0.65 Number of scatterers: 3522 At special positions: 0 Unit cell: (128.96, 112.32, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 666 8.00 N 648 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 489.4 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 305 through 308 removed outlier: 6.530A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA3, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.268A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.451A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 347 removed outlier: 6.351A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS E 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 356 removed outlier: 6.500A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.710A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 367 through 379 removed outlier: 6.213A pdb=" N ASN A 368 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE E 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ARG E 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 378 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 305 through 308 removed outlier: 6.520A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.276A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.442A pdb=" N GLN B 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 343 through 347 removed outlier: 6.361A pdb=" N LEU B 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS F 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE B 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 351 through 356 removed outlier: 6.492A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER D 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY B 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER B 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.720A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 367 through 379 removed outlier: 6.207A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG F 379 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 0.78 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 600 1.31 - 1.44: 812 1.44 - 1.56: 1955 1.56 - 1.68: 203 1.68 - 1.80: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CA ILE F 354 " pdb=" CB ILE F 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.04e+01 bond pdb=" CA ILE D 354 " pdb=" CB ILE D 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.03e+01 bond pdb=" CA ILE E 354 " pdb=" CB ILE E 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.02e+01 bond pdb=" CA ILE B 354 " pdb=" CB ILE B 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.02e+01 bond pdb=" CA ILE A 354 " pdb=" CB ILE A 354 " ideal model delta sigma weight residual 1.533 1.602 -0.069 1.26e-02 6.30e+03 3.00e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 103.05 - 108.83: 271 108.83 - 114.60: 2015 114.60 - 120.37: 942 120.37 - 126.14: 1500 126.14 - 131.91: 54 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C VAL E 363 " pdb=" N PRO E 364 " pdb=" CA PRO E 364 " ideal model delta sigma weight residual 119.76 115.90 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C VAL A 363 " pdb=" N PRO A 364 " pdb=" CA PRO A 364 " ideal model delta sigma weight residual 119.76 115.91 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C VAL C 363 " pdb=" N PRO C 364 " pdb=" CA PRO C 364 " ideal model delta sigma weight residual 119.76 115.92 3.84 1.00e+00 1.00e+00 1.48e+01 angle pdb=" C VAL B 363 " pdb=" N PRO B 364 " pdb=" CA PRO B 364 " ideal model delta sigma weight residual 119.76 115.93 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C VAL F 363 " pdb=" N PRO F 364 " pdb=" CA PRO F 364 " ideal model delta sigma weight residual 119.76 115.94 3.82 1.00e+00 1.00e+00 1.46e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.04: 1782 11.04 - 22.06: 258 22.06 - 33.09: 78 33.09 - 44.11: 48 44.11 - 55.14: 12 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" C THR C 377 " pdb=" N THR C 377 " pdb=" CA THR C 377 " pdb=" CB THR C 377 " ideal model delta harmonic sigma weight residual -122.00 -129.71 7.71 0 2.50e+00 1.60e-01 9.52e+00 dihedral pdb=" C THR E 377 " pdb=" N THR E 377 " pdb=" CA THR E 377 " pdb=" CB THR E 377 " ideal model delta harmonic sigma weight residual -122.00 -129.69 7.69 0 2.50e+00 1.60e-01 9.47e+00 dihedral pdb=" C THR F 377 " pdb=" N THR F 377 " pdb=" CA THR F 377 " pdb=" CB THR F 377 " ideal model delta harmonic sigma weight residual -122.00 -129.68 7.68 0 2.50e+00 1.60e-01 9.43e+00 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 218 0.061 - 0.120: 179 0.120 - 0.179: 83 0.179 - 0.238: 42 0.238 - 0.297: 12 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " 0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE E 346 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE F 346 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.010 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE A 346 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.003 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1308 2.96 - 3.44: 3136 3.44 - 3.93: 5345 3.93 - 4.41: 5628 4.41 - 4.90: 10743 Nonbonded interactions: 26160 Sorted by model distance: nonbonded pdb=" O VAL B 313 " pdb=" OD1 ASP B 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL E 313 " pdb=" OD1 ASP E 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL A 313 " pdb=" OD1 ASP A 314 " model vdw 2.474 3.040 nonbonded pdb=" O VAL D 313 " pdb=" OD1 ASP D 314 " model vdw 2.475 3.040 nonbonded pdb=" O VAL F 313 " pdb=" OD1 ASP F 314 " model vdw 2.475 3.040 ... (remaining 26155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.900 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: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.660 Find NCS groups from input model: 0.230 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.019 0.071 3576 Z= 1.226 Angle : 1.469 10.790 4782 Z= 0.757 Chirality : 0.105 0.297 534 Planarity : 0.012 0.062 612 Dihedral : 13.340 55.136 1374 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.006 HIS E 374 PHE 0.048 0.017 PHE E 346 TYR 0.040 0.011 TYR C 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.427 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: A 307 GLN cc_start: 0.7970 (mt0) cc_final: 0.7720 (mp10) REVERT: A 340 LYS cc_start: 0.8053 (mttt) cc_final: 0.7668 (mtpp) REVERT: A 369 LYS cc_start: 0.8889 (ptpt) cc_final: 0.8624 (ptpp) REVERT: B 369 LYS cc_start: 0.8847 (ptpt) cc_final: 0.8521 (ptpp) REVERT: C 369 LYS cc_start: 0.8809 (ptpt) cc_final: 0.8443 (ptpp) REVERT: D 321 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8263 (mmtp) REVERT: D 331 LYS cc_start: 0.8503 (tttt) cc_final: 0.8193 (tttt) REVERT: E 321 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7959 (mmtp) REVERT: F 311 LYS cc_start: 0.8353 (mttt) cc_final: 0.8051 (mmtt) REVERT: F 321 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7988 (mmtp) REVERT: F 369 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8544 (ptpp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2782 time to fit residues: 41.8463 Evaluate side-chains 121 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN C 307 GLN D 362 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3576 Z= 0.311 Angle : 0.760 11.201 4782 Z= 0.353 Chirality : 0.052 0.128 534 Planarity : 0.004 0.031 612 Dihedral : 5.512 16.530 474 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.74 % Allowed : 11.69 % Favored : 86.57 % 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: -3.67 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.009 0.002 PHE B 378 TYR 0.015 0.003 TYR A 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8055 (mt0) cc_final: 0.7839 (mp10) REVERT: A 376 LEU cc_start: 0.8580 (tp) cc_final: 0.8359 (tp) REVERT: B 307 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 342 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8028 (mm-30) REVERT: B 349 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7806 (mtm180) REVERT: B 369 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8581 (mtmt) REVERT: C 369 LYS cc_start: 0.8682 (ptpt) cc_final: 0.8318 (ptpp) REVERT: D 321 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8271 (mmtp) REVERT: D 331 LYS cc_start: 0.8399 (tttt) cc_final: 0.8188 (tttt) REVERT: E 321 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7765 (mmtp) REVERT: F 317 LYS cc_start: 0.7920 (ptmt) cc_final: 0.7685 (ptpt) REVERT: F 321 LYS cc_start: 0.8454 (mtpt) cc_final: 0.7944 (mmtp) REVERT: F 331 LYS cc_start: 0.8463 (tttt) cc_final: 0.8102 (ttmm) REVERT: F 349 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7972 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 139 average time/residue: 0.2491 time to fit residues: 39.0690 Evaluate side-chains 130 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 327 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.0040 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 374 HIS F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3576 Z= 0.169 Angle : 0.638 9.717 4782 Z= 0.293 Chirality : 0.051 0.122 534 Planarity : 0.004 0.027 612 Dihedral : 4.701 14.212 474 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.74 % Allowed : 14.93 % Favored : 83.33 % 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: -3.27 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.008 0.002 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 305 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (t) REVERT: A 336 GLN cc_start: 0.8101 (tt0) cc_final: 0.7646 (tt0) REVERT: B 307 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 342 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 369 LYS cc_start: 0.8976 (ptpt) cc_final: 0.8575 (mtmt) REVERT: C 342 GLU cc_start: 0.4988 (pm20) cc_final: 0.4582 (pm20) REVERT: C 369 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8174 (ptpp) REVERT: D 321 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8253 (mmtp) REVERT: D 331 LYS cc_start: 0.8401 (tttt) cc_final: 0.8073 (tttt) REVERT: E 311 LYS cc_start: 0.8579 (mtmt) cc_final: 0.7601 (mmtt) REVERT: E 321 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7713 (mmtp) REVERT: F 311 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8129 (mmtt) REVERT: F 317 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7789 (ptpt) REVERT: F 321 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7965 (mmtp) REVERT: F 331 LYS cc_start: 0.8414 (tttt) cc_final: 0.8210 (tttp) REVERT: F 347 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8342 (mttp) REVERT: F 349 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7982 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2623 time to fit residues: 35.1441 Evaluate side-chains 114 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 377 THR 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: 2.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN D 307 GLN D 368 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3576 Z= 0.429 Angle : 0.793 9.051 4782 Z= 0.375 Chirality : 0.054 0.128 534 Planarity : 0.004 0.024 612 Dihedral : 5.773 18.192 474 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.98 % Allowed : 13.68 % Favored : 82.34 % 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: -3.44 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 329 PHE 0.012 0.003 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.419 Fit side-chains REVERT: A 340 LYS cc_start: 0.8164 (mttt) cc_final: 0.7602 (mtpp) REVERT: B 307 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 368 ASN cc_start: 0.8702 (m110) cc_final: 0.8484 (m-40) REVERT: B 369 LYS cc_start: 0.9072 (ptpt) cc_final: 0.8652 (mtmt) REVERT: C 369 LYS cc_start: 0.8718 (ptpt) cc_final: 0.8312 (ptpp) REVERT: D 321 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8355 (mmtp) REVERT: D 331 LYS cc_start: 0.8353 (tttt) cc_final: 0.7970 (tttt) REVERT: D 338 GLU cc_start: 0.7911 (tt0) cc_final: 0.7684 (tt0) REVERT: E 321 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7727 (mmtp) REVERT: F 321 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8061 (mmtp) REVERT: F 331 LYS cc_start: 0.8533 (tttt) cc_final: 0.8290 (tttp) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.2359 time to fit residues: 35.8435 Evaluate side-chains 125 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3576 Z= 0.198 Angle : 0.647 8.003 4782 Z= 0.302 Chirality : 0.051 0.126 534 Planarity : 0.004 0.029 612 Dihedral : 4.894 16.668 474 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.73 % Allowed : 15.67 % Favored : 80.60 % 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: -3.23 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.008 0.002 PHE D 346 TYR 0.014 0.002 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) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.451 Fit side-chains REVERT: A 307 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7668 (mp10) REVERT: A 340 LYS cc_start: 0.8189 (mttt) cc_final: 0.7612 (mtpp) REVERT: B 307 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 342 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 349 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8159 (mtm180) REVERT: B 369 LYS cc_start: 0.9061 (ptpt) cc_final: 0.8652 (mtmt) REVERT: C 369 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8222 (ptpp) REVERT: D 321 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8336 (mmtp) REVERT: D 331 LYS cc_start: 0.8298 (tttt) cc_final: 0.7900 (tttt) REVERT: E 321 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7668 (mmtp) REVERT: F 321 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8007 (mmtp) REVERT: F 331 LYS cc_start: 0.8585 (tttt) cc_final: 0.8329 (tttt) REVERT: F 375 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7966 (ttmt) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 0.2572 time to fit residues: 36.7351 Evaluate side-chains 125 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3576 Z= 0.275 Angle : 0.691 9.572 4782 Z= 0.321 Chirality : 0.051 0.127 534 Planarity : 0.004 0.034 612 Dihedral : 5.112 16.650 474 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.48 % Allowed : 17.66 % Favored : 78.86 % 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: -3.24 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE B 378 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.428 Fit side-chains REVERT: A 340 LYS cc_start: 0.8229 (mttt) cc_final: 0.7642 (mtpp) REVERT: A 376 LEU cc_start: 0.8618 (tp) cc_final: 0.8415 (tp) REVERT: B 307 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7946 (mp10) REVERT: B 349 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8213 (mtm180) REVERT: B 368 ASN cc_start: 0.8681 (m110) cc_final: 0.8468 (m-40) REVERT: B 369 LYS cc_start: 0.9051 (ptpt) cc_final: 0.8646 (mtmt) REVERT: C 369 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8264 (ptpp) REVERT: D 321 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8373 (mmtp) REVERT: D 331 LYS cc_start: 0.8271 (tttt) cc_final: 0.7873 (tttt) REVERT: E 321 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7737 (mmtp) REVERT: F 311 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8052 (mmtt) REVERT: F 321 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8038 (mmtp) REVERT: F 375 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7859 (ttmt) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.2622 time to fit residues: 34.4667 Evaluate side-chains 117 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3576 Z= 0.235 Angle : 0.657 9.193 4782 Z= 0.307 Chirality : 0.051 0.128 534 Planarity : 0.004 0.034 612 Dihedral : 4.980 15.824 474 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.48 % Allowed : 19.40 % Favored : 77.11 % 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: -3.25 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.009 0.002 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.431 Fit side-chains REVERT: A 307 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7572 (mp10) REVERT: A 340 LYS cc_start: 0.8219 (mttt) cc_final: 0.7622 (mtpp) REVERT: A 376 LEU cc_start: 0.8600 (tp) cc_final: 0.8378 (tp) REVERT: B 307 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7949 (mp10) REVERT: B 349 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8220 (mtm180) REVERT: B 369 LYS cc_start: 0.9058 (ptpt) cc_final: 0.8629 (mtmt) REVERT: C 369 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8264 (ptpp) REVERT: D 321 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8402 (mmtp) REVERT: D 331 LYS cc_start: 0.8257 (tttt) cc_final: 0.7859 (tttt) REVERT: E 311 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8398 (mmtt) REVERT: E 321 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7710 (mmtp) REVERT: F 311 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8043 (mmtt) REVERT: F 321 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8066 (mmtp) REVERT: F 375 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7844 (ttmt) outliers start: 14 outliers final: 14 residues processed: 118 average time/residue: 0.2653 time to fit residues: 35.2935 Evaluate side-chains 119 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3576 Z= 0.289 Angle : 0.687 9.331 4782 Z= 0.322 Chirality : 0.051 0.128 534 Planarity : 0.004 0.033 612 Dihedral : 5.178 16.881 474 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.23 % Allowed : 18.91 % Favored : 76.87 % 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: -3.27 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE B 378 TYR 0.016 0.003 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.431 Fit side-chains REVERT: A 340 LYS cc_start: 0.8217 (mttt) cc_final: 0.7618 (mtpp) REVERT: A 376 LEU cc_start: 0.8628 (tp) cc_final: 0.8421 (tp) REVERT: B 307 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7897 (mp10) REVERT: B 349 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8227 (mtm180) REVERT: B 368 ASN cc_start: 0.8687 (m110) cc_final: 0.8480 (m-40) REVERT: B 369 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8791 (mtmt) REVERT: C 369 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8270 (ptpp) REVERT: D 321 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8440 (mmtp) REVERT: D 331 LYS cc_start: 0.8244 (tttt) cc_final: 0.8036 (tttt) REVERT: E 311 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8500 (mmtt) REVERT: E 321 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7757 (mmtp) REVERT: F 311 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8133 (mmtt) REVERT: F 321 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8086 (mmtp) REVERT: F 375 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7799 (ttmt) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.2766 time to fit residues: 36.7979 Evaluate side-chains 118 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.004 0.022 3576 Z= 0.287 Angle : 0.686 9.222 4782 Z= 0.323 Chirality : 0.051 0.129 534 Planarity : 0.004 0.033 612 Dihedral : 5.200 16.776 474 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.73 % Allowed : 20.15 % Favored : 76.12 % 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: -3.32 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.010 0.002 PHE B 378 TYR 0.016 0.003 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.438 Fit side-chains REVERT: A 307 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7465 (mp10) REVERT: A 309 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 376 LEU cc_start: 0.8583 (tp) cc_final: 0.8378 (tp) REVERT: B 307 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7882 (mp10) REVERT: B 349 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8105 (mtm180) REVERT: B 368 ASN cc_start: 0.8654 (m110) cc_final: 0.8442 (m-40) REVERT: B 369 LYS cc_start: 0.9024 (ptpt) cc_final: 0.8705 (mtmt) REVERT: C 369 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8278 (ptpp) REVERT: D 321 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8448 (mmtp) REVERT: E 311 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8529 (mmtt) REVERT: E 321 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7753 (mmtp) REVERT: F 311 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8125 (mmtt) REVERT: F 321 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8157 (mmtp) REVERT: F 375 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7834 (ttmt) outliers start: 15 outliers final: 13 residues processed: 114 average time/residue: 0.2642 time to fit residues: 33.9767 Evaluate side-chains 114 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0030 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3576 Z= 0.336 Angle : 0.724 9.315 4782 Z= 0.341 Chirality : 0.051 0.129 534 Planarity : 0.004 0.041 612 Dihedral : 5.377 17.668 474 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.73 % Allowed : 21.39 % Favored : 74.88 % 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: -3.40 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.011 0.002 PHE B 378 TYR 0.015 0.003 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) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.389 Fit side-chains REVERT: B 307 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7893 (mp10) REVERT: B 349 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8186 (mtm180) REVERT: B 368 ASN cc_start: 0.8703 (m110) cc_final: 0.8473 (m-40) REVERT: B 369 LYS cc_start: 0.9015 (ptpt) cc_final: 0.8751 (mtmt) REVERT: C 369 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8376 (ptpp) REVERT: D 321 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8457 (mmtp) REVERT: E 311 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8538 (mmtt) REVERT: E 321 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7793 (mmtp) REVERT: F 311 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8139 (mmtt) REVERT: F 321 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8179 (mmtp) REVERT: F 375 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7825 (ttmt) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.2577 time to fit residues: 34.5639 Evaluate side-chains 120 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.158193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.139255 restraints weight = 4684.088| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.12 r_work: 0.3973 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3576 Z= 0.174 Angle : 0.626 9.032 4782 Z= 0.295 Chirality : 0.050 0.125 534 Planarity : 0.004 0.043 612 Dihedral : 4.759 14.886 474 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.48 % Allowed : 21.89 % Favored : 74.63 % 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: -3.22 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.008 0.002 PHE D 346 TYR 0.019 0.003 TYR A 310 ARG 0.002 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.93 seconds wall clock time: 25 minutes 17.34 seconds (1517.34 seconds total)