Starting phenix.real_space_refine on Wed Jan 17 22:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/01_2024/8q8w_18263.pdb" } resolution = 2.85 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= 0.002 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 2034 2.51 5 N 594 2.21 5 O 612 1.98 5 H 3372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.58, per 1000 atoms: 0.54 Number of scatterers: 6618 At special positions: 0 Unit cell: (121.952, 140.904, 45.32, 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 612 8.00 N 594 7.00 C 2034 6.00 H 3372 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 - 3.50 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: 5.51 Conformation dependent library (CDL) restraints added in 761.1 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.620A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.702A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.363A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS C 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.546A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.518A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL E 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.397A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.592A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.771A pdb=" N ASP A 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 374 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.522A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.305A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.606A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 removed outlier: 6.777A pdb=" N GLY B 333 " --> pdb=" O GLY D 334 " (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: 6.592A 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: 6.290A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.273A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.376A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 231 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: 2.14 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3366 1.12 - 1.29: 546 1.29 - 1.47: 1076 1.47 - 1.64: 1675 1.64 - 1.81: 6 Bond restraints: 6669 Sorted by residual: bond pdb=" NE2 GLN E 336 " pdb="HE22 GLN E 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 326 " pdb=" H GLY B 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY C 333 " pdb=" H GLY C 333 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 327 " pdb="HD21 ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY A 355 " pdb=" H GLY A 355 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 95.96 - 102.61: 23 102.61 - 109.26: 4362 109.26 - 115.90: 4371 115.90 - 122.55: 2731 122.55 - 129.20: 681 Bond angle restraints: 12168 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" OE1 GLN F 336 " pdb=" CD GLN F 336 " pdb=" NE2 GLN F 336 " ideal model delta sigma weight residual 122.60 117.91 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" OE1 GLN D 336 " pdb=" CD GLN D 336 " pdb=" NE2 GLN D 336 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 2665 13.72 - 27.45: 157 27.45 - 41.17: 50 41.17 - 54.89: 22 54.89 - 68.61: 64 Dihedral angle restraints: 2958 sinusoidal: 1644 harmonic: 1314 Sorted by residual: dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU D 372 " pdb=" C GLU D 372 " pdb=" N THR D 373 " pdb=" CA THR D 373 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU F 372 " pdb=" C GLU F 372 " pdb=" N THR F 373 " pdb=" CA THR F 373 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 220 0.053 - 0.106: 180 0.106 - 0.160: 61 0.160 - 0.213: 26 0.213 - 0.266: 8 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA SER B 352 " pdb=" N SER B 352 " pdb=" C SER B 352 " pdb=" CB SER B 352 " 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 F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 492 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.052 2.00e-02 2.50e+03 4.88e-02 3.58e+01 pdb=" CG ASN A 368 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.048 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.035 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " -0.061 2.00e-02 2.50e+03 3.69e-02 3.06e+01 pdb=" CG HIS D 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 362 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS D 362 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 HIS D 362 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.066 2.00e-02 2.50e+03 2.96e-02 2.62e+01 pdb=" CG TYR E 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.058 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.002 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 395 2.14 - 2.76: 10601 2.76 - 3.37: 17256 3.37 - 3.99: 23349 3.99 - 4.60: 32273 Nonbonded interactions: 83874 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.526 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.553 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.614 1.850 ... (remaining 83869 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' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) } 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: 4.920 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: 0.090 Extract box with map and model: 13.300 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 26.290 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 0.035 3297 Z= 0.715 Angle : 1.754 6.483 4410 Z= 1.171 Chirality : 0.085 0.266 495 Planarity : 0.009 0.034 561 Dihedral : 11.104 67.181 1263 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.38 (0.35), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 330 PHE 0.051 0.020 PHE F 346 TYR 0.061 0.013 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) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8013 (mttt) cc_final: 0.7209 (mtpp) REVERT: C 340 LYS cc_start: 0.8388 (mttt) cc_final: 0.7772 (mtpp) REVERT: C 343 LYS cc_start: 0.8441 (mttt) cc_final: 0.8221 (mttp) REVERT: C 370 LYS cc_start: 0.7613 (tttt) cc_final: 0.7329 (ttpt) REVERT: B 321 LYS cc_start: 0.7034 (mttt) cc_final: 0.6649 (mttt) REVERT: B 336 GLN cc_start: 0.7457 (tt0) cc_final: 0.7246 (tt0) REVERT: B 340 LYS cc_start: 0.6971 (mttt) cc_final: 0.6574 (mtpp) REVERT: A 317 LYS cc_start: 0.7134 (mttt) cc_final: 0.6503 (mtpp) REVERT: A 340 LYS cc_start: 0.7295 (mttt) cc_final: 0.6722 (mtpp) REVERT: A 375 LYS cc_start: 0.7016 (tttt) cc_final: 0.6776 (ttpp) REVERT: D 314 ASP cc_start: 0.7989 (t0) cc_final: 0.7645 (t0) REVERT: D 317 LYS cc_start: 0.8030 (mttt) cc_final: 0.7675 (mttm) REVERT: D 336 GLN cc_start: 0.7876 (tt0) cc_final: 0.7591 (tt0) REVERT: D 338 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 340 LYS cc_start: 0.7769 (mttt) cc_final: 0.7447 (mtpp) REVERT: D 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.8103 (tttt) REVERT: E 317 LYS cc_start: 0.6968 (mttt) cc_final: 0.6166 (mtpp) REVERT: E 340 LYS cc_start: 0.7166 (mttt) cc_final: 0.6568 (mtpp) REVERT: E 347 LYS cc_start: 0.8436 (mttt) cc_final: 0.8188 (mttm) REVERT: F 311 LYS cc_start: 0.8233 (mttt) cc_final: 0.7177 (mttm) REVERT: F 317 LYS cc_start: 0.6777 (mttt) cc_final: 0.6569 (mtmt) REVERT: F 336 GLN cc_start: 0.7466 (tt0) cc_final: 0.6999 (tt0) REVERT: F 340 LYS cc_start: 0.7054 (mttt) cc_final: 0.6796 (mtpp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 3.1245 time to fit residues: 382.6738 Evaluate side-chains 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 327 ASN D 307 GLN D 327 ASN F 307 GLN F 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3297 Z= 0.253 Angle : 0.574 5.996 4410 Z= 0.295 Chirality : 0.049 0.124 495 Planarity : 0.004 0.028 561 Dihedral : 6.151 15.946 435 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 10.22 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.001 PHE D 346 TYR 0.008 0.001 TYR B 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8042 (t0) cc_final: 0.7569 (t0) REVERT: C 317 LYS cc_start: 0.8047 (mttt) cc_final: 0.7243 (mtpp) REVERT: C 340 LYS cc_start: 0.8374 (mttt) cc_final: 0.7785 (mtpp) REVERT: C 347 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: C 370 LYS cc_start: 0.7620 (tttt) cc_final: 0.7278 (ttpt) REVERT: B 336 GLN cc_start: 0.7383 (tt0) cc_final: 0.7138 (tt0) REVERT: B 340 LYS cc_start: 0.6981 (mttt) cc_final: 0.6618 (mtpp) REVERT: B 342 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7071 (tt0) REVERT: A 317 LYS cc_start: 0.7229 (mttt) cc_final: 0.6658 (mtpp) REVERT: A 324 SER cc_start: 0.8331 (t) cc_final: 0.8089 (t) REVERT: A 340 LYS cc_start: 0.7345 (mttt) cc_final: 0.6760 (mtpp) REVERT: A 375 LYS cc_start: 0.6998 (tttt) cc_final: 0.6784 (ttpp) REVERT: D 314 ASP cc_start: 0.8076 (t0) cc_final: 0.7862 (t0) REVERT: D 317 LYS cc_start: 0.8065 (mttt) cc_final: 0.7721 (mttm) REVERT: D 338 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 340 LYS cc_start: 0.7762 (mttt) cc_final: 0.7436 (mtpp) REVERT: D 353 LYS cc_start: 0.7574 (mttt) cc_final: 0.6925 (tttp) REVERT: D 375 LYS cc_start: 0.8394 (tttt) cc_final: 0.8081 (tttt) REVERT: E 317 LYS cc_start: 0.7061 (mttt) cc_final: 0.6245 (mtpp) REVERT: E 340 LYS cc_start: 0.7276 (mttt) cc_final: 0.6672 (mtpp) REVERT: E 345 ASP cc_start: 0.7815 (m-30) cc_final: 0.7445 (t0) REVERT: E 347 LYS cc_start: 0.8347 (mttt) cc_final: 0.8108 (mttm) REVERT: F 311 LYS cc_start: 0.8228 (mttt) cc_final: 0.7106 (mttm) REVERT: F 336 GLN cc_start: 0.7391 (tt0) cc_final: 0.6875 (tt0) REVERT: F 340 LYS cc_start: 0.7080 (mttt) cc_final: 0.6809 (mtpp) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 3.4247 time to fit residues: 283.1041 Evaluate side-chains 76 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3297 Z= 0.277 Angle : 0.524 5.948 4410 Z= 0.269 Chirality : 0.050 0.127 495 Planarity : 0.003 0.021 561 Dihedral : 5.434 15.503 435 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.61 % Allowed : 10.22 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.002 PHE B 346 TYR 0.011 0.002 TYR B 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8030 (mttt) cc_final: 0.7241 (mtpp) REVERT: C 340 LYS cc_start: 0.8400 (mttt) cc_final: 0.7796 (mtpp) REVERT: C 347 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: B 314 ASP cc_start: 0.7950 (t0) cc_final: 0.7584 (t0) REVERT: B 336 GLN cc_start: 0.7364 (tt0) cc_final: 0.7113 (tt0) REVERT: B 340 LYS cc_start: 0.6934 (mttt) cc_final: 0.6578 (mtpp) REVERT: B 353 LYS cc_start: 0.6962 (mttt) cc_final: 0.6184 (tttp) REVERT: A 317 LYS cc_start: 0.7328 (mttt) cc_final: 0.6733 (mtpp) REVERT: A 340 LYS cc_start: 0.7408 (mttt) cc_final: 0.6810 (mtpp) REVERT: A 345 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7309 (t0) REVERT: D 317 LYS cc_start: 0.8035 (mttt) cc_final: 0.7679 (mttp) REVERT: D 340 LYS cc_start: 0.7755 (mttt) cc_final: 0.7420 (mtpp) REVERT: D 375 LYS cc_start: 0.8466 (tttt) cc_final: 0.8151 (tttt) REVERT: E 314 ASP cc_start: 0.8294 (t70) cc_final: 0.8076 (t70) REVERT: E 317 LYS cc_start: 0.7002 (mttt) cc_final: 0.6175 (mtpp) REVERT: E 340 LYS cc_start: 0.7268 (mttt) cc_final: 0.6671 (mtpp) REVERT: E 345 ASP cc_start: 0.7893 (m-30) cc_final: 0.7524 (t0) REVERT: F 311 LYS cc_start: 0.8227 (mttt) cc_final: 0.7115 (mttm) REVERT: F 336 GLN cc_start: 0.7435 (tt0) cc_final: 0.6942 (tt0) REVERT: F 340 LYS cc_start: 0.7063 (mttt) cc_final: 0.6779 (mtpp) REVERT: F 353 LYS cc_start: 0.7241 (mttt) cc_final: 0.6419 (tttp) outliers start: 6 outliers final: 0 residues processed: 74 average time/residue: 3.1622 time to fit residues: 239.1421 Evaluate side-chains 66 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3297 Z= 0.193 Angle : 0.471 6.159 4410 Z= 0.239 Chirality : 0.050 0.126 495 Planarity : 0.003 0.020 561 Dihedral : 5.035 15.320 435 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 11.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.006 0.001 PHE B 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8066 (mttt) cc_final: 0.7292 (mtpp) REVERT: C 340 LYS cc_start: 0.8423 (mttt) cc_final: 0.7816 (mtpp) REVERT: C 347 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: B 314 ASP cc_start: 0.7992 (t0) cc_final: 0.7630 (t0) REVERT: B 336 GLN cc_start: 0.7301 (tt0) cc_final: 0.7068 (tt0) REVERT: B 340 LYS cc_start: 0.6909 (mttt) cc_final: 0.6560 (mtpp) REVERT: A 317 LYS cc_start: 0.7302 (mttt) cc_final: 0.6738 (mtpp) REVERT: A 340 LYS cc_start: 0.7415 (mttt) cc_final: 0.6808 (mtpp) REVERT: A 345 ASP cc_start: 0.7996 (m-30) cc_final: 0.7459 (t0) REVERT: D 317 LYS cc_start: 0.8024 (mttt) cc_final: 0.7667 (mttm) REVERT: D 340 LYS cc_start: 0.7768 (mttt) cc_final: 0.7426 (mtpp) REVERT: D 353 LYS cc_start: 0.7569 (mttt) cc_final: 0.6915 (tttp) REVERT: D 375 LYS cc_start: 0.8467 (tttt) cc_final: 0.8151 (tttt) REVERT: E 314 ASP cc_start: 0.8323 (t70) cc_final: 0.8065 (t70) REVERT: E 317 LYS cc_start: 0.7167 (mttt) cc_final: 0.6371 (mtpp) REVERT: E 340 LYS cc_start: 0.7220 (mttt) cc_final: 0.6591 (mtpt) REVERT: E 345 ASP cc_start: 0.7894 (m-30) cc_final: 0.7467 (t0) REVERT: F 311 LYS cc_start: 0.8222 (mttt) cc_final: 0.7115 (mttm) REVERT: F 336 GLN cc_start: 0.7364 (tt0) cc_final: 0.6906 (tt0) REVERT: F 340 LYS cc_start: 0.7066 (mttt) cc_final: 0.6757 (mtpp) outliers start: 4 outliers final: 1 residues processed: 69 average time/residue: 3.2621 time to fit residues: 229.8964 Evaluate side-chains 63 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.110 Angle : 0.436 6.121 4410 Z= 0.219 Chirality : 0.051 0.127 495 Planarity : 0.002 0.017 561 Dihedral : 4.660 14.141 435 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.81 % Allowed : 12.90 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.004 0.001 PHE B 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8040 (mttt) cc_final: 0.7286 (mtpp) REVERT: C 340 LYS cc_start: 0.8395 (mttt) cc_final: 0.7797 (mtpp) REVERT: C 347 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8289 (mttm) REVERT: B 340 LYS cc_start: 0.6851 (mttt) cc_final: 0.6497 (mtpp) REVERT: A 317 LYS cc_start: 0.7284 (mttt) cc_final: 0.6743 (mtpp) REVERT: A 340 LYS cc_start: 0.7389 (mttt) cc_final: 0.6788 (mtpp) REVERT: A 345 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7432 (t0) REVERT: D 317 LYS cc_start: 0.7999 (mttt) cc_final: 0.7631 (mttm) REVERT: D 340 LYS cc_start: 0.7787 (mttt) cc_final: 0.7445 (mtpp) REVERT: D 353 LYS cc_start: 0.7571 (mttt) cc_final: 0.6933 (tttp) REVERT: D 375 LYS cc_start: 0.8471 (tttt) cc_final: 0.8155 (tttt) REVERT: E 314 ASP cc_start: 0.8324 (t70) cc_final: 0.8026 (t70) REVERT: E 317 LYS cc_start: 0.7214 (mttt) cc_final: 0.6413 (mtpp) REVERT: E 340 LYS cc_start: 0.7225 (mttt) cc_final: 0.6585 (mtpt) REVERT: E 345 ASP cc_start: 0.7841 (m-30) cc_final: 0.7433 (t0) REVERT: F 311 LYS cc_start: 0.8167 (mttt) cc_final: 0.7064 (mttm) REVERT: F 336 GLN cc_start: 0.7306 (tt0) cc_final: 0.6845 (tt0) REVERT: F 340 LYS cc_start: 0.7035 (mttt) cc_final: 0.6724 (mtpp) outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 3.2239 time to fit residues: 223.9153 Evaluate side-chains 66 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3297 Z= 0.311 Angle : 0.486 5.999 4410 Z= 0.249 Chirality : 0.049 0.125 495 Planarity : 0.003 0.018 561 Dihedral : 4.873 14.742 435 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.81 % Allowed : 13.98 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.009 0.002 PHE D 346 TYR 0.011 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.552 Fit side-chains REVERT: C 314 ASP cc_start: 0.8201 (t70) cc_final: 0.7741 (t70) REVERT: C 317 LYS cc_start: 0.8011 (mttt) cc_final: 0.7257 (mtpp) REVERT: C 340 LYS cc_start: 0.8435 (mttt) cc_final: 0.7843 (mtpp) REVERT: C 347 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8373 (mtmm) REVERT: B 321 LYS cc_start: 0.7103 (mttt) cc_final: 0.6818 (mttt) REVERT: B 340 LYS cc_start: 0.6848 (mttt) cc_final: 0.6519 (mtpp) REVERT: B 342 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7179 (tt0) REVERT: B 353 LYS cc_start: 0.6986 (mttt) cc_final: 0.6333 (tttp) REVERT: A 317 LYS cc_start: 0.7228 (mttt) cc_final: 0.6667 (mtpp) REVERT: A 340 LYS cc_start: 0.7450 (mttt) cc_final: 0.6830 (mtpp) REVERT: A 345 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7375 (t0) REVERT: D 317 LYS cc_start: 0.8037 (mttt) cc_final: 0.7659 (mttm) REVERT: D 340 LYS cc_start: 0.7813 (mttt) cc_final: 0.7426 (mtpp) REVERT: D 353 LYS cc_start: 0.7586 (mttt) cc_final: 0.6925 (tttp) REVERT: D 375 LYS cc_start: 0.8477 (tttt) cc_final: 0.8170 (tttt) REVERT: E 317 LYS cc_start: 0.7222 (mttt) cc_final: 0.6450 (mtpp) REVERT: E 340 LYS cc_start: 0.7240 (mttt) cc_final: 0.6564 (mtpt) REVERT: E 345 ASP cc_start: 0.7859 (m-30) cc_final: 0.7457 (t0) REVERT: F 311 LYS cc_start: 0.8230 (mttt) cc_final: 0.7136 (mttm) REVERT: F 336 GLN cc_start: 0.7373 (tt0) cc_final: 0.6943 (tt0) REVERT: F 340 LYS cc_start: 0.7057 (mttt) cc_final: 0.6715 (mtpp) REVERT: F 353 LYS cc_start: 0.7154 (mttt) cc_final: 0.6422 (tttp) outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 3.4587 time to fit residues: 239.5670 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.124 Angle : 0.439 5.962 4410 Z= 0.221 Chirality : 0.051 0.127 495 Planarity : 0.002 0.024 561 Dihedral : 4.621 14.522 435 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 14.52 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 374 PHE 0.005 0.001 PHE B 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8221 (t70) cc_final: 0.7695 (t70) REVERT: C 317 LYS cc_start: 0.8020 (mttt) cc_final: 0.7270 (mtpp) REVERT: C 340 LYS cc_start: 0.8392 (mttt) cc_final: 0.7733 (mtpt) REVERT: C 347 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8247 (mttm) REVERT: B 340 LYS cc_start: 0.6833 (mttt) cc_final: 0.6503 (mtpp) REVERT: B 342 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 317 LYS cc_start: 0.7364 (mttt) cc_final: 0.6791 (mtpp) REVERT: A 340 LYS cc_start: 0.7471 (mttt) cc_final: 0.6859 (mtpp) REVERT: A 345 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7362 (t0) REVERT: D 317 LYS cc_start: 0.7996 (mttt) cc_final: 0.7622 (mttm) REVERT: D 340 LYS cc_start: 0.7786 (mttt) cc_final: 0.7410 (mtpp) REVERT: D 353 LYS cc_start: 0.7567 (mttt) cc_final: 0.6948 (tttp) REVERT: E 317 LYS cc_start: 0.7242 (mttt) cc_final: 0.6479 (mtpp) REVERT: E 340 LYS cc_start: 0.7210 (mttt) cc_final: 0.6550 (mtpt) REVERT: E 345 ASP cc_start: 0.7843 (m-30) cc_final: 0.7439 (t0) REVERT: F 311 LYS cc_start: 0.8211 (mttt) cc_final: 0.7113 (mttm) REVERT: F 336 GLN cc_start: 0.7307 (tt0) cc_final: 0.6865 (tt0) REVERT: F 340 LYS cc_start: 0.7014 (mttt) cc_final: 0.6684 (mtpp) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 3.6157 time to fit residues: 239.7324 Evaluate side-chains 66 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.0000 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3297 Z= 0.103 Angle : 0.410 5.559 4410 Z= 0.205 Chirality : 0.051 0.127 495 Planarity : 0.003 0.037 561 Dihedral : 4.217 13.186 435 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.08 % Allowed : 14.25 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 362 PHE 0.001 0.000 PHE B 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8150 (t70) cc_final: 0.7735 (t70) REVERT: C 317 LYS cc_start: 0.8018 (mttt) cc_final: 0.7324 (mtpp) REVERT: C 340 LYS cc_start: 0.8352 (mttt) cc_final: 0.7772 (mtpp) REVERT: C 347 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8224 (mttm) REVERT: B 340 LYS cc_start: 0.6787 (mttt) cc_final: 0.6466 (mtpp) REVERT: B 342 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7211 (tt0) REVERT: A 317 LYS cc_start: 0.7480 (mttt) cc_final: 0.6840 (mtpp) REVERT: A 340 LYS cc_start: 0.7457 (mttt) cc_final: 0.6854 (mtpp) REVERT: A 345 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7342 (t0) REVERT: D 317 LYS cc_start: 0.7977 (mttt) cc_final: 0.7591 (mttp) REVERT: D 340 LYS cc_start: 0.7803 (mttt) cc_final: 0.7465 (mtpp) REVERT: D 353 LYS cc_start: 0.7562 (mttt) cc_final: 0.6939 (tttp) REVERT: E 317 LYS cc_start: 0.7198 (mttt) cc_final: 0.6439 (mtpp) REVERT: E 340 LYS cc_start: 0.7206 (mttt) cc_final: 0.6544 (mtpt) REVERT: E 345 ASP cc_start: 0.7811 (m-30) cc_final: 0.7432 (t0) REVERT: F 311 LYS cc_start: 0.8173 (mttt) cc_final: 0.7084 (mttm) REVERT: F 336 GLN cc_start: 0.7198 (tt0) cc_final: 0.6760 (tt0) REVERT: F 340 LYS cc_start: 0.7010 (mttt) cc_final: 0.6679 (mtpp) outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 3.2128 time to fit residues: 242.7922 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3297 Z= 0.181 Angle : 0.434 5.287 4410 Z= 0.217 Chirality : 0.049 0.124 495 Planarity : 0.003 0.042 561 Dihedral : 4.348 13.478 435 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 15.32 % Favored : 83.87 % 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: -0.68 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.007 0.001 PHE F 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8171 (t70) cc_final: 0.7720 (t70) REVERT: C 317 LYS cc_start: 0.7982 (mttt) cc_final: 0.7294 (mtpp) REVERT: C 340 LYS cc_start: 0.8383 (mttt) cc_final: 0.7802 (mtpp) REVERT: B 340 LYS cc_start: 0.6817 (mttt) cc_final: 0.6495 (mtpp) REVERT: B 342 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7175 (tt0) REVERT: A 317 LYS cc_start: 0.7441 (mttt) cc_final: 0.6824 (mtpp) REVERT: A 340 LYS cc_start: 0.7499 (mttt) cc_final: 0.6873 (mtpp) REVERT: A 345 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7299 (t0) REVERT: D 317 LYS cc_start: 0.7995 (mttt) cc_final: 0.7607 (mttm) REVERT: D 340 LYS cc_start: 0.7774 (mttt) cc_final: 0.7398 (mtpp) REVERT: D 353 LYS cc_start: 0.7575 (mttt) cc_final: 0.6951 (tttp) REVERT: E 317 LYS cc_start: 0.7250 (mttt) cc_final: 0.6496 (mtpp) REVERT: E 340 LYS cc_start: 0.7212 (mttt) cc_final: 0.6550 (mtpt) REVERT: E 345 ASP cc_start: 0.7825 (m-30) cc_final: 0.7432 (t0) REVERT: F 311 LYS cc_start: 0.8197 (mttt) cc_final: 0.7104 (mttm) REVERT: F 336 GLN cc_start: 0.7278 (tt0) cc_final: 0.6852 (tt0) REVERT: F 340 LYS cc_start: 0.7061 (mttt) cc_final: 0.6716 (mtpp) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 3.5086 time to fit residues: 250.3814 Evaluate side-chains 68 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.125 Angle : 0.418 5.064 4410 Z= 0.209 Chirality : 0.050 0.125 495 Planarity : 0.003 0.048 561 Dihedral : 4.226 13.027 435 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 15.32 % Favored : 83.60 % 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: -0.71 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 362 PHE 0.004 0.001 PHE B 346 TYR 0.006 0.001 TYR E 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8163 (t70) cc_final: 0.7712 (t70) REVERT: C 317 LYS cc_start: 0.7971 (mttt) cc_final: 0.7281 (mtpp) REVERT: C 340 LYS cc_start: 0.8405 (mttt) cc_final: 0.7741 (mtpt) REVERT: B 340 LYS cc_start: 0.6794 (mttt) cc_final: 0.6471 (mtpp) REVERT: B 342 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7174 (tt0) REVERT: A 311 LYS cc_start: 0.8556 (pttt) cc_final: 0.8298 (pttt) REVERT: A 317 LYS cc_start: 0.7451 (mttt) cc_final: 0.6837 (mtpp) REVERT: A 340 LYS cc_start: 0.7518 (mttt) cc_final: 0.6881 (mtpp) REVERT: A 345 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7309 (t0) REVERT: D 317 LYS cc_start: 0.7980 (mttt) cc_final: 0.7584 (mttm) REVERT: D 340 LYS cc_start: 0.7780 (mttt) cc_final: 0.7406 (mtpp) REVERT: D 353 LYS cc_start: 0.7572 (mttt) cc_final: 0.6959 (tttp) REVERT: E 317 LYS cc_start: 0.7231 (mttt) cc_final: 0.6501 (mtpp) REVERT: E 340 LYS cc_start: 0.7216 (mttt) cc_final: 0.6560 (mtpt) REVERT: E 345 ASP cc_start: 0.7816 (m-30) cc_final: 0.7425 (t0) REVERT: F 311 LYS cc_start: 0.8186 (mttt) cc_final: 0.7100 (mttm) REVERT: F 336 GLN cc_start: 0.7266 (tt0) cc_final: 0.6841 (tt0) REVERT: F 340 LYS cc_start: 0.7065 (mttt) cc_final: 0.6726 (mtpp) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 3.3979 time to fit residues: 235.8537 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.115186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106837 restraints weight = 13748.075| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.58 r_work: 0.3541 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3297 Z= 0.127 Angle : 0.418 4.826 4410 Z= 0.209 Chirality : 0.050 0.124 495 Planarity : 0.003 0.051 561 Dihedral : 4.152 11.821 435 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.54 % Allowed : 16.40 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 374 PHE 0.004 0.001 PHE F 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5068.65 seconds wall clock time: 89 minutes 38.89 seconds (5378.89 seconds total)