Starting phenix.real_space_refine on Mon Mar 11 02:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/03_2024/8q8w_18263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/03_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_18263/03_2024/8q8w_18263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/03_2024/8q8w_18263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/03_2024/8q8w_18263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/03_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-dev-5265/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: 3.40, per 1000 atoms: 0.51 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: 5.33 Conformation dependent library (CDL) restraints added in 722.7 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: 0.68 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: 2.19 Time building geometry restraints manager: 5.61 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: 2696 13.72 - 27.45: 179 27.45 - 41.17: 69 41.17 - 54.89: 56 54.89 - 68.61: 72 Dihedral angle restraints: 3072 sinusoidal: 1758 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 3069 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: 8.640 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: 0.000 Extract box with map and model: 11.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.420 Find NCS groups from input model: 0.330 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:17.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.370 ------------------------------------------------------------------------------- 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 : 0.590 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: 3.0468 time to fit residues: 373.1891 Evaluate side-chains 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN D 327 ASN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3297 Z= 0.195 Angle : 0.579 6.034 4410 Z= 0.300 Chirality : 0.051 0.135 495 Planarity : 0.004 0.028 561 Dihedral : 6.161 16.011 435 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 0.76 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: -0.97 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.007 0.001 PHE D 346 TYR 0.009 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 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8011 (t0) cc_final: 0.7559 (t0) REVERT: C 317 LYS cc_start: 0.8033 (mttt) cc_final: 0.7237 (mtpp) REVERT: C 340 LYS cc_start: 0.8342 (mttt) cc_final: 0.7744 (mtpp) REVERT: C 343 LYS cc_start: 0.8356 (mttt) cc_final: 0.8152 (mttp) REVERT: C 347 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8338 (mtmm) REVERT: C 370 LYS cc_start: 0.7604 (tttt) cc_final: 0.7259 (ttpt) REVERT: B 336 GLN cc_start: 0.7370 (tt0) cc_final: 0.7150 (tt0) REVERT: B 340 LYS cc_start: 0.6978 (mttt) cc_final: 0.6615 (mtpp) REVERT: B 342 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7047 (tt0) REVERT: A 317 LYS cc_start: 0.7210 (mttt) cc_final: 0.6635 (mtpp) REVERT: A 324 SER cc_start: 0.8327 (t) cc_final: 0.8068 (t) REVERT: A 340 LYS cc_start: 0.7327 (mttt) cc_final: 0.6751 (mtpp) REVERT: A 375 LYS cc_start: 0.6995 (tttt) cc_final: 0.6780 (ttpp) REVERT: D 314 ASP cc_start: 0.8063 (t0) cc_final: 0.7851 (t0) REVERT: D 317 LYS cc_start: 0.8049 (mttt) cc_final: 0.7705 (mttm) REVERT: D 340 LYS cc_start: 0.7744 (mttt) cc_final: 0.7422 (mtpp) REVERT: D 353 LYS cc_start: 0.7571 (mttt) cc_final: 0.6917 (tttp) REVERT: D 375 LYS cc_start: 0.8389 (tttt) cc_final: 0.8076 (tttt) REVERT: E 317 LYS cc_start: 0.7001 (mttt) cc_final: 0.6202 (mtpp) REVERT: E 340 LYS cc_start: 0.7268 (mttt) cc_final: 0.6666 (mtpp) REVERT: E 345 ASP cc_start: 0.7846 (m-30) cc_final: 0.7453 (t0) REVERT: E 347 LYS cc_start: 0.8327 (mttt) cc_final: 0.8110 (mttm) REVERT: F 311 LYS cc_start: 0.8236 (mttt) cc_final: 0.7125 (mttm) REVERT: F 336 GLN cc_start: 0.7363 (tt0) cc_final: 0.6855 (tt0) REVERT: F 340 LYS cc_start: 0.7080 (mttt) cc_final: 0.6826 (mtpp) outliers start: 3 outliers final: 0 residues processed: 82 average time/residue: 3.3596 time to fit residues: 280.9087 Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 336 GLN F 307 GLN F 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3297 Z= 0.222 Angle : 0.509 6.104 4410 Z= 0.262 Chirality : 0.051 0.127 495 Planarity : 0.003 0.023 561 Dihedral : 5.463 15.338 435 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.34 % Allowed : 10.48 % 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: -0.87 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.008 0.001 PHE B 346 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 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 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8019 (mttt) cc_final: 0.7249 (mtpp) REVERT: C 340 LYS cc_start: 0.8376 (mttt) cc_final: 0.7776 (mtpp) REVERT: C 343 LYS cc_start: 0.8360 (mttt) cc_final: 0.8157 (mttp) REVERT: C 347 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: C 370 LYS cc_start: 0.7541 (tttt) cc_final: 0.7179 (ttpt) REVERT: B 314 ASP cc_start: 0.7896 (t0) cc_final: 0.7535 (t0) REVERT: B 336 GLN cc_start: 0.7381 (tt0) cc_final: 0.7123 (tt0) REVERT: B 340 LYS cc_start: 0.6958 (mttt) cc_final: 0.6591 (mtpp) REVERT: B 342 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7097 (tt0) REVERT: B 353 LYS cc_start: 0.6946 (mttt) cc_final: 0.6160 (tttp) REVERT: A 317 LYS cc_start: 0.7322 (mttt) cc_final: 0.6743 (mtpp) REVERT: A 340 LYS cc_start: 0.7369 (mttt) cc_final: 0.6784 (mtpp) REVERT: A 345 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7321 (t0) REVERT: A 375 LYS cc_start: 0.7027 (tttt) cc_final: 0.6807 (ttpp) REVERT: D 317 LYS cc_start: 0.8035 (mttt) cc_final: 0.7681 (mttp) REVERT: D 340 LYS cc_start: 0.7785 (mttt) cc_final: 0.7457 (mtpp) REVERT: D 375 LYS cc_start: 0.8447 (tttt) cc_final: 0.8136 (tttt) REVERT: E 314 ASP cc_start: 0.8218 (t70) cc_final: 0.8000 (t70) REVERT: E 317 LYS cc_start: 0.6992 (mttt) cc_final: 0.6145 (mtpp) REVERT: E 340 LYS cc_start: 0.7271 (mttt) cc_final: 0.6664 (mtpp) REVERT: E 345 ASP cc_start: 0.7837 (m-30) cc_final: 0.7455 (t0) REVERT: E 347 LYS cc_start: 0.8353 (mttt) cc_final: 0.8098 (mttm) REVERT: F 311 LYS cc_start: 0.8257 (mttt) cc_final: 0.7147 (mttm) REVERT: F 336 GLN cc_start: 0.7417 (tt0) cc_final: 0.6925 (tt0) REVERT: F 340 LYS cc_start: 0.7067 (mttt) cc_final: 0.6760 (mtpp) outliers start: 5 outliers final: 0 residues processed: 81 average time/residue: 3.2726 time to fit residues: 270.8731 Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3297 Z= 0.273 Angle : 0.503 6.049 4410 Z= 0.259 Chirality : 0.050 0.126 495 Planarity : 0.003 0.019 561 Dihedral : 5.220 15.432 435 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.88 % Allowed : 11.56 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.010 0.002 PHE D 346 TYR 0.010 0.002 TYR B 310 ARG 0.002 0.000 ARG D 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 80 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8025 (mttt) cc_final: 0.7243 (mtpp) REVERT: C 340 LYS cc_start: 0.8413 (mttt) cc_final: 0.7804 (mtpp) REVERT: C 343 LYS cc_start: 0.8337 (mttt) cc_final: 0.8119 (mttp) REVERT: C 347 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8351 (mtmm) REVERT: C 370 LYS cc_start: 0.7553 (tttt) cc_final: 0.7154 (ttpt) REVERT: B 314 ASP cc_start: 0.7987 (t0) cc_final: 0.7623 (t0) REVERT: B 336 GLN cc_start: 0.7373 (tt0) cc_final: 0.7124 (tt0) REVERT: B 340 LYS cc_start: 0.6926 (mttt) cc_final: 0.6569 (mtpp) REVERT: A 317 LYS cc_start: 0.7273 (mttt) cc_final: 0.6690 (mtpp) REVERT: A 340 LYS cc_start: 0.7405 (mttt) cc_final: 0.6794 (mtpp) REVERT: A 345 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7284 (t0) REVERT: A 347 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: D 317 LYS cc_start: 0.8050 (mttt) cc_final: 0.7683 (mttm) REVERT: D 340 LYS cc_start: 0.7790 (mttt) cc_final: 0.7445 (mtpp) REVERT: D 375 LYS cc_start: 0.8486 (tttt) cc_final: 0.8170 (tttt) REVERT: E 314 ASP cc_start: 0.8398 (t70) cc_final: 0.8104 (t70) REVERT: E 317 LYS cc_start: 0.7208 (mttt) cc_final: 0.6416 (mtpp) REVERT: E 340 LYS cc_start: 0.7220 (mttt) cc_final: 0.6588 (mtpt) REVERT: E 345 ASP cc_start: 0.7831 (m-30) cc_final: 0.7412 (t0) REVERT: E 347 LYS cc_start: 0.8343 (mttt) cc_final: 0.8075 (mttm) REVERT: F 311 LYS cc_start: 0.8215 (mttt) cc_final: 0.7121 (mttm) REVERT: F 336 GLN cc_start: 0.7412 (tt0) cc_final: 0.6941 (tt0) REVERT: F 340 LYS cc_start: 0.7065 (mttt) cc_final: 0.6748 (mtpp) REVERT: F 353 LYS cc_start: 0.7252 (mttt) cc_final: 0.6402 (tttp) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 3.3636 time to fit residues: 267.6301 Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 347 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 336 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3439 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= 0.129 Angle : 0.448 6.075 4410 Z= 0.227 Chirality : 0.051 0.128 495 Planarity : 0.003 0.020 561 Dihedral : 4.841 14.792 435 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 12.63 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 C 329 PHE 0.005 0.001 PHE B 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG C 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 76 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8042 (mttt) cc_final: 0.7270 (mtpp) REVERT: C 340 LYS cc_start: 0.8391 (mttt) cc_final: 0.7727 (mtpt) REVERT: C 343 LYS cc_start: 0.8343 (mttt) cc_final: 0.8125 (mttp) REVERT: C 347 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: C 370 LYS cc_start: 0.7523 (tttt) cc_final: 0.7165 (ttpt) REVERT: B 314 ASP cc_start: 0.8022 (t0) cc_final: 0.7612 (t0) REVERT: B 336 GLN cc_start: 0.7281 (tt0) cc_final: 0.7004 (tt0) REVERT: B 340 LYS cc_start: 0.6899 (mttt) cc_final: 0.6545 (mtpp) REVERT: B 353 LYS cc_start: 0.6996 (mttt) cc_final: 0.6306 (tttp) REVERT: A 317 LYS cc_start: 0.7304 (mttt) cc_final: 0.6750 (mtpp) REVERT: A 340 LYS cc_start: 0.7370 (mttt) cc_final: 0.6777 (mtpp) REVERT: A 345 ASP cc_start: 0.7967 (m-30) cc_final: 0.7394 (t0) REVERT: D 317 LYS cc_start: 0.8008 (mttt) cc_final: 0.7646 (mttm) REVERT: D 340 LYS cc_start: 0.7806 (mttt) cc_final: 0.7465 (mtpp) REVERT: D 342 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7855 (tt0) REVERT: D 353 LYS cc_start: 0.7569 (mttt) cc_final: 0.6931 (tttp) REVERT: D 375 LYS cc_start: 0.8474 (tttt) cc_final: 0.8156 (tttt) REVERT: E 314 ASP cc_start: 0.8358 (t70) cc_final: 0.8061 (t70) REVERT: E 317 LYS cc_start: 0.7208 (mttt) cc_final: 0.6395 (mtpp) REVERT: E 340 LYS cc_start: 0.7214 (mttt) cc_final: 0.6596 (mtpt) REVERT: E 345 ASP cc_start: 0.7838 (m-30) cc_final: 0.7440 (t0) REVERT: E 347 LYS cc_start: 0.8359 (mttt) cc_final: 0.8119 (mttm) REVERT: F 311 LYS cc_start: 0.8166 (mttt) cc_final: 0.7057 (mttm) REVERT: F 336 GLN cc_start: 0.7328 (tt0) cc_final: 0.6894 (tt0) REVERT: F 340 LYS cc_start: 0.7081 (mttt) cc_final: 0.6761 (mtpp) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 3.5020 time to fit residues: 271.2351 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS 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: 4.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3297 Z= 0.199 Angle : 0.446 5.491 4410 Z= 0.227 Chirality : 0.050 0.127 495 Planarity : 0.003 0.030 561 Dihedral : 4.714 14.342 435 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.76 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: -0.65 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.006 0.001 PHE F 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG D 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 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8217 (t70) cc_final: 0.7744 (t70) REVERT: C 317 LYS cc_start: 0.8008 (mttt) cc_final: 0.7266 (mtpp) REVERT: C 340 LYS cc_start: 0.8380 (mttt) cc_final: 0.7787 (mtpp) REVERT: C 343 LYS cc_start: 0.8326 (mttt) cc_final: 0.8108 (mttp) REVERT: C 347 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8361 (mtmm) REVERT: C 370 LYS cc_start: 0.7520 (tttt) cc_final: 0.7191 (ttpt) REVERT: B 321 LYS cc_start: 0.7087 (mttt) cc_final: 0.6796 (mttt) REVERT: B 336 GLN cc_start: 0.7341 (tt0) cc_final: 0.7059 (tt0) REVERT: B 340 LYS cc_start: 0.6862 (mttt) cc_final: 0.6521 (mtpp) REVERT: A 317 LYS cc_start: 0.7239 (mttt) cc_final: 0.6681 (mtpp) REVERT: A 340 LYS cc_start: 0.7426 (mttt) cc_final: 0.6821 (mtpp) REVERT: A 345 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7290 (t0) REVERT: D 317 LYS cc_start: 0.8008 (mttt) cc_final: 0.7628 (mttp) REVERT: D 340 LYS cc_start: 0.7790 (mttt) cc_final: 0.7404 (mtpp) REVERT: D 353 LYS cc_start: 0.7593 (mttt) cc_final: 0.6938 (tttp) REVERT: D 375 LYS cc_start: 0.8475 (tttt) cc_final: 0.8170 (tttt) REVERT: E 314 ASP cc_start: 0.8383 (t70) cc_final: 0.8118 (t70) REVERT: E 317 LYS cc_start: 0.7228 (mttt) cc_final: 0.6444 (mtpp) REVERT: E 340 LYS cc_start: 0.7250 (mttt) cc_final: 0.6587 (mtpt) REVERT: E 345 ASP cc_start: 0.7821 (m-30) cc_final: 0.7477 (t0) REVERT: F 311 LYS cc_start: 0.8210 (mttt) cc_final: 0.7110 (mttm) REVERT: F 336 GLN cc_start: 0.7324 (tt0) cc_final: 0.6843 (tt0) REVERT: F 340 LYS cc_start: 0.7080 (mttt) cc_final: 0.6743 (mtpp) REVERT: F 353 LYS cc_start: 0.7164 (mttt) cc_final: 0.6448 (tttm) outliers start: 3 outliers final: 0 residues processed: 73 average time/residue: 3.5695 time to fit residues: 265.5664 Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN D 336 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3297 Z= 0.166 Angle : 0.441 5.630 4410 Z= 0.224 Chirality : 0.050 0.126 495 Planarity : 0.003 0.033 561 Dihedral : 4.599 14.293 435 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 13.71 % Favored : 85.48 % 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: -0.66 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.006 0.001 PHE B 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG E 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 73 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8214 (t70) cc_final: 0.7736 (t70) REVERT: C 317 LYS cc_start: 0.8012 (mttt) cc_final: 0.7273 (mtpp) REVERT: C 340 LYS cc_start: 0.8376 (mttt) cc_final: 0.7786 (mtpp) REVERT: C 343 LYS cc_start: 0.8328 (mttt) cc_final: 0.8108 (mttp) REVERT: C 370 LYS cc_start: 0.7499 (tttt) cc_final: 0.7193 (ttpt) REVERT: B 321 LYS cc_start: 0.7063 (mttt) cc_final: 0.6764 (mttt) REVERT: B 336 GLN cc_start: 0.7317 (tt0) cc_final: 0.7039 (tt0) REVERT: B 340 LYS cc_start: 0.6856 (mttt) cc_final: 0.6516 (mtpp) REVERT: B 342 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7187 (tt0) REVERT: A 317 LYS cc_start: 0.7222 (mttt) cc_final: 0.6671 (mtpp) REVERT: A 340 LYS cc_start: 0.7458 (mttt) cc_final: 0.6848 (mtpp) REVERT: A 345 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7301 (t0) REVERT: D 317 LYS cc_start: 0.8004 (mttt) cc_final: 0.7630 (mttm) REVERT: D 340 LYS cc_start: 0.7822 (mttt) cc_final: 0.7441 (mtpp) REVERT: D 353 LYS cc_start: 0.7573 (mttt) cc_final: 0.6949 (tttp) REVERT: E 317 LYS cc_start: 0.7201 (mttt) cc_final: 0.6384 (mtpp) REVERT: E 340 LYS cc_start: 0.7250 (mttt) cc_final: 0.6587 (mtpt) REVERT: E 345 ASP cc_start: 0.7866 (m-30) cc_final: 0.7460 (t0) REVERT: F 311 LYS cc_start: 0.8214 (mttt) cc_final: 0.7114 (mttm) REVERT: F 336 GLN cc_start: 0.7318 (tt0) cc_final: 0.6879 (tt0) REVERT: F 340 LYS cc_start: 0.7077 (mttt) cc_final: 0.6738 (mtpp) REVERT: F 353 LYS cc_start: 0.7147 (mttt) cc_final: 0.6449 (tttm) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 3.6564 time to fit residues: 264.9549 Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3876 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= 0.109 Angle : 0.414 5.401 4410 Z= 0.209 Chirality : 0.051 0.126 495 Planarity : 0.003 0.040 561 Dihedral : 4.345 13.464 435 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.54 % Allowed : 14.52 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.46 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 374 PHE 0.003 0.000 PHE B 346 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG D 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 76 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8190 (t70) cc_final: 0.7787 (t70) REVERT: C 317 LYS cc_start: 0.7979 (mttt) cc_final: 0.7264 (mtpp) REVERT: C 340 LYS cc_start: 0.8359 (mttt) cc_final: 0.7707 (mtpt) REVERT: C 343 LYS cc_start: 0.8317 (mttt) cc_final: 0.8102 (mttp) REVERT: C 370 LYS cc_start: 0.7481 (tttt) cc_final: 0.7156 (ttpt) REVERT: B 336 GLN cc_start: 0.7237 (tt0) cc_final: 0.6887 (tt0) REVERT: B 340 LYS cc_start: 0.6796 (mttt) cc_final: 0.6468 (mtpp) REVERT: B 342 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7153 (tt0) REVERT: A 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.6813 (mtpp) REVERT: A 340 LYS cc_start: 0.7471 (mttt) cc_final: 0.6866 (mtpp) REVERT: A 345 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7318 (t0) REVERT: D 317 LYS cc_start: 0.7981 (mttt) cc_final: 0.7601 (mttm) REVERT: D 340 LYS cc_start: 0.7807 (mttt) cc_final: 0.7427 (mtpp) REVERT: D 353 LYS cc_start: 0.7546 (mttt) cc_final: 0.6957 (tttp) REVERT: E 317 LYS cc_start: 0.7179 (mttt) cc_final: 0.6409 (mtpp) REVERT: E 340 LYS cc_start: 0.7235 (mttt) cc_final: 0.6582 (mtpt) REVERT: E 345 ASP cc_start: 0.7825 (m-30) cc_final: 0.7435 (t0) REVERT: F 311 LYS cc_start: 0.8186 (mttt) cc_final: 0.7090 (mttm) REVERT: F 336 GLN cc_start: 0.7292 (tt0) cc_final: 0.6795 (tt0) REVERT: F 340 LYS cc_start: 0.7043 (mttt) cc_final: 0.6705 (mtpp) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 3.5071 time to fit residues: 264.7466 Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3297 Z= 0.191 Angle : 0.433 5.179 4410 Z= 0.219 Chirality : 0.050 0.124 495 Planarity : 0.003 0.043 561 Dihedral : 4.450 13.711 435 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.27 % Allowed : 15.32 % Favored : 84.41 % 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: -0.60 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (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 C 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 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8188 (t70) cc_final: 0.7712 (t70) REVERT: C 317 LYS cc_start: 0.7978 (mttt) cc_final: 0.7288 (mtpp) REVERT: C 340 LYS cc_start: 0.8381 (mttt) cc_final: 0.7800 (mtpp) REVERT: C 343 LYS cc_start: 0.8319 (mttt) cc_final: 0.8101 (mttp) REVERT: B 336 GLN cc_start: 0.7305 (tt0) cc_final: 0.7033 (tt0) REVERT: B 340 LYS cc_start: 0.6814 (mttt) cc_final: 0.6493 (mtpp) REVERT: B 342 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7166 (tt0) REVERT: A 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.6792 (mtpp) REVERT: A 340 LYS cc_start: 0.7473 (mttt) cc_final: 0.6863 (mtpp) REVERT: A 345 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7299 (t0) REVERT: D 317 LYS cc_start: 0.8000 (mttt) cc_final: 0.7603 (mttm) REVERT: D 340 LYS cc_start: 0.7825 (mttt) cc_final: 0.7440 (mtpp) REVERT: D 353 LYS cc_start: 0.7621 (mttt) cc_final: 0.6979 (tttp) REVERT: E 317 LYS cc_start: 0.7177 (mttt) cc_final: 0.6427 (mtpp) REVERT: E 340 LYS cc_start: 0.7238 (mttt) cc_final: 0.6578 (mtpt) REVERT: E 345 ASP cc_start: 0.7827 (m-30) cc_final: 0.7445 (t0) REVERT: F 311 LYS cc_start: 0.8207 (mttt) cc_final: 0.7114 (mttm) REVERT: F 336 GLN cc_start: 0.7382 (tt0) cc_final: 0.6924 (tt0) REVERT: F 340 LYS cc_start: 0.7047 (mttt) cc_final: 0.6702 (mtpp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 3.5242 time to fit residues: 248.0289 Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4053 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= 0.118 Angle : 0.414 4.900 4410 Z= 0.208 Chirality : 0.051 0.126 495 Planarity : 0.003 0.048 561 Dihedral : 4.267 12.988 435 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.27 % Allowed : 15.32 % Favored : 84.41 % 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: -0.62 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.46 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 374 PHE 0.004 0.001 PHE F 346 TYR 0.006 0.001 TYR E 310 ARG 0.001 0.000 ARG D 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 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8175 (t70) cc_final: 0.7731 (t70) REVERT: C 317 LYS cc_start: 0.7991 (mttt) cc_final: 0.7302 (mtpp) REVERT: C 340 LYS cc_start: 0.8381 (mttt) cc_final: 0.7720 (mtpt) REVERT: C 343 LYS cc_start: 0.8312 (mttt) cc_final: 0.8096 (mttp) REVERT: B 336 GLN cc_start: 0.7214 (tt0) cc_final: 0.6834 (tt0) REVERT: B 340 LYS cc_start: 0.6816 (mttt) cc_final: 0.6490 (mtpp) REVERT: B 342 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7163 (tt0) REVERT: B 349 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7404 (mtt180) REVERT: A 317 LYS cc_start: 0.7423 (mttt) cc_final: 0.6825 (mtpp) REVERT: A 340 LYS cc_start: 0.7481 (mttt) cc_final: 0.6865 (mtpp) REVERT: A 345 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7301 (t0) REVERT: D 317 LYS cc_start: 0.7989 (mttt) cc_final: 0.7593 (mttm) REVERT: D 340 LYS cc_start: 0.7807 (mttt) cc_final: 0.7433 (mtpp) REVERT: D 353 LYS cc_start: 0.7592 (mttt) cc_final: 0.6974 (tttp) REVERT: E 317 LYS cc_start: 0.7242 (mttt) cc_final: 0.6508 (mtpp) REVERT: E 340 LYS cc_start: 0.7253 (mttt) cc_final: 0.6607 (mtpt) REVERT: E 345 ASP cc_start: 0.7817 (m-30) cc_final: 0.7436 (t0) REVERT: F 311 LYS cc_start: 0.8167 (mttt) cc_final: 0.7067 (mttm) REVERT: F 336 GLN cc_start: 0.7341 (tt0) cc_final: 0.6906 (tt0) REVERT: F 340 LYS cc_start: 0.7046 (mttt) cc_final: 0.6702 (mtpp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 3.3293 time to fit residues: 237.8721 Evaluate side-chains 70 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 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: 3.9990 chunk 26 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107593 restraints weight = 13694.029| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.61 r_work: 0.3526 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3297 Z= 0.129 Angle : 0.403 4.535 4410 Z= 0.203 Chirality : 0.050 0.124 495 Planarity : 0.003 0.053 561 Dihedral : 4.118 11.053 435 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.54 % Allowed : 15.05 % Favored : 84.41 % 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: -0.61 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.46 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 362 PHE 0.005 0.001 PHE F 346 TYR 0.006 0.001 TYR E 310 ARG 0.000 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5220.90 seconds wall clock time: 91 minutes 44.66 seconds (5504.66 seconds total)