Starting phenix.real_space_refine on Fri Aug 2 20:44:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttl_41610/08_2024/8ttl_41610_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1590 2.51 5 N 465 2.21 5 O 522 1.98 5 H 2607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5190 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "C" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "D" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "F" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Time building chain proxies: 6.26, per 1000 atoms: 1.21 Number of scatterers: 5190 At special positions: 0 Unit cell: (105.457, 88.29, 35.1525, 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 522 8.00 N 465 7.00 C 1590 6.00 H 2607 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: 4.10 Conformation dependent library (CDL) restraints added in 771.0 milliseconds 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.909A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 360 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 361 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS A 362 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 360 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 361 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS B 362 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 379 removed outlier: 6.326A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386 removed outlier: 6.162A pdb=" N LYS A 385 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.699A pdb=" N GLU B 391 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR C 394 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 393 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.593A pdb=" N VAL A 398 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 398 " --> pdb=" O VAL C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 420 removed outlier: 9.161A pdb=" N ASN A 410 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N SER B 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N SER A 412 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N GLY B 415 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 414 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE B 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 416 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N MET B 419 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP A 418 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 410 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 411 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 412 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER C 413 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 414 " --> pdb=" O SER C 413 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 415 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 427 Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 439 Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.421A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE F 308 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.442A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 319 Processing sheet with id=AB3, first strand: chain 'D' and resid 324 through 325 removed outlier: 6.540A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 329 32 hydrogen bonds defined for protein. 96 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: 1.76 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.34 - 0.63: 4 0.63 - 0.93: 60 0.93 - 1.23: 2833 1.23 - 1.52: 1458 1.52 - 1.82: 871 Warning: very small bond lengths. Bond restraints: 5226 Sorted by residual: bond pdb=" OG1 THR D 319 " pdb=" HG1 THR D 319 " ideal model delta sigma weight residual 0.840 0.339 0.501 2.00e-02 2.50e+03 6.28e+02 bond pdb=" OG SER C 416 " pdb=" HG SER C 416 " ideal model delta sigma weight residual 0.840 0.369 0.471 2.00e-02 2.50e+03 5.55e+02 bond pdb=" OG SER C 352 " pdb=" HG SER C 352 " ideal model delta sigma weight residual 0.840 0.453 0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" OG SER B 413 " pdb=" HG SER B 413 " ideal model delta sigma weight residual 0.840 0.546 0.294 2.00e-02 2.50e+03 2.15e+02 bond pdb=" OG SER B 409 " pdb=" HG SER B 409 " ideal model delta sigma weight residual 0.840 0.645 0.195 2.00e-02 2.50e+03 9.54e+01 ... (remaining 5221 not shown) Histogram of bond angle deviations from ideal: 95.41 - 106.63: 492 106.63 - 117.86: 6889 117.86 - 129.08: 2098 129.08 - 140.30: 3 140.30 - 151.53: 1 Bond angle restraints: 9483 Sorted by residual: angle pdb=" CB THR D 319 " pdb=" OG1 THR D 319 " pdb=" HG1 THR D 319 " ideal model delta sigma weight residual 110.00 151.53 -41.53 3.00e+00 1.11e-01 1.92e+02 angle pdb=" CB SER C 416 " pdb=" OG SER C 416 " pdb=" HG SER C 416 " ideal model delta sigma weight residual 110.00 134.84 -24.84 3.00e+00 1.11e-01 6.85e+01 angle pdb=" CB SER B 413 " pdb=" OG SER B 413 " pdb=" HG SER B 413 " ideal model delta sigma weight residual 110.00 131.00 -21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" CA ASP B 418 " pdb=" CB ASP B 418 " pdb=" CG ASP B 418 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA ASP C 418 " pdb=" CB ASP C 418 " pdb=" CG ASP C 418 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.13e+01 ... (remaining 9478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 2116 14.87 - 29.74: 184 29.74 - 44.61: 63 44.61 - 59.48: 67 59.48 - 74.35: 27 Dihedral angle restraints: 2457 sinusoidal: 1377 harmonic: 1080 Sorted by residual: dihedral pdb=" CA THR C 386 " pdb=" C THR C 386 " pdb=" N ASP C 387 " pdb=" CA ASP C 387 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA THR D 319 " pdb=" C THR D 319 " pdb=" N SER D 320 " pdb=" CA SER D 320 " ideal model delta harmonic sigma weight residual -180.00 -154.31 -25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 2454 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.082: 200 0.082 - 0.162: 129 0.162 - 0.243: 63 0.243 - 0.323: 19 0.323 - 0.404: 9 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA THR B 386 " pdb=" N THR B 386 " pdb=" C THR B 386 " pdb=" CB THR B 386 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA GLU C 380 " pdb=" N GLU C 380 " pdb=" C GLU C 380 " pdb=" CB GLU C 380 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA HIS B 388 " pdb=" N HIS B 388 " pdb=" C HIS B 388 " pdb=" CB HIS B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 417 not shown) Planarity restraints: 783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 388 " -0.140 2.00e-02 2.50e+03 7.82e-02 1.37e+02 pdb=" CG HIS A 388 " 0.114 2.00e-02 2.50e+03 pdb=" ND1 HIS A 388 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 HIS A 388 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 HIS A 388 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS A 388 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS A 388 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 HIS A 388 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 HIS A 388 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " -0.102 2.00e-02 2.50e+03 5.46e-02 6.71e+01 pdb=" CG HIS C 362 " 0.096 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 HIS C 362 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS C 362 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS C 362 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " -0.065 2.00e-02 2.50e+03 6.67e-02 6.66e+01 pdb=" CG ASN A 359 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " -0.018 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.097 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " -0.089 2.00e-02 2.50e+03 ... (remaining 780 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 566 2.23 - 2.82: 9642 2.82 - 3.42: 13479 3.42 - 4.01: 18228 4.01 - 4.60: 26002 Nonbonded interactions: 67917 Sorted by model distance: nonbonded pdb=" O ALA B 382 " pdb=" HG1 THR B 427 " model vdw 1.642 2.450 nonbonded pdb=" HZ1 LYS B 395 " pdb=" OD2 ASP B 430 " model vdw 1.708 2.450 nonbonded pdb=" O ALA C 382 " pdb=" HG1 THR C 427 " model vdw 1.712 2.450 nonbonded pdb=" OE1 GLU B 431 " pdb=" HZ2 LYS B 438 " model vdw 1.727 2.450 nonbonded pdb=" HZ1 LYS A 395 " pdb=" OD2 ASP A 430 " model vdw 1.746 2.450 ... (remaining 67912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.660 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: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.830 Find NCS groups from input model: 0.130 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.013 0.074 2619 Z= 0.903 Angle : 2.136 8.399 3534 Z= 1.403 Chirality : 0.133 0.404 420 Planarity : 0.013 0.078 453 Dihedral : 13.165 74.355 963 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.08 % Favored : 92.04 % Rotamer: Outliers : 1.35 % Allowed : 4.38 % Favored : 94.28 % Cbeta Deviations : 2.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.33), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.006 HIS B 388 PHE 0.057 0.020 PHE A 378 TYR 0.081 0.028 TYR D 310 ARG 0.009 0.003 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 2.3499 time to fit residues: 201.8898 Evaluate side-chains 50 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2619 Z= 0.181 Angle : 0.627 4.710 3534 Z= 0.341 Chirality : 0.051 0.137 420 Planarity : 0.004 0.056 453 Dihedral : 7.107 19.225 357 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.68 % Allowed : 16.16 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.34), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.012 0.002 PHE A 378 TYR 0.009 0.002 TYR E 310 ARG 0.007 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.453 Fit side-chains REVERT: C 385 LYS cc_start: 0.8025 (tttm) cc_final: 0.7808 (tttt) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 2.9716 time to fit residues: 181.7633 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2619 Z= 0.130 Angle : 0.522 3.978 3534 Z= 0.278 Chirality : 0.050 0.136 420 Planarity : 0.004 0.058 453 Dihedral : 6.094 18.431 357 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.68 % Allowed : 17.17 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.36), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.007 0.001 PHE A 378 TYR 0.006 0.001 TYR E 310 ARG 0.010 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.451 Fit side-chains REVERT: C 385 LYS cc_start: 0.8107 (tttm) cc_final: 0.7878 (tttt) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 2.8197 time to fit residues: 166.8923 Evaluate side-chains 56 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 31 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2619 Z= 0.120 Angle : 0.490 3.837 3534 Z= 0.261 Chirality : 0.050 0.136 420 Planarity : 0.004 0.066 453 Dihedral : 5.769 18.009 357 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.69 % Allowed : 18.52 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.004 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.010 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: C 385 LYS cc_start: 0.8126 (tttm) cc_final: 0.7911 (tttt) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 3.3313 time to fit residues: 200.1310 Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2619 Z= 0.153 Angle : 0.506 4.059 3534 Z= 0.270 Chirality : 0.050 0.135 420 Planarity : 0.004 0.068 453 Dihedral : 5.777 18.827 357 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.03 % Allowed : 17.85 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.006 0.001 PHE A 378 TYR 0.006 0.001 TYR D 310 ARG 0.010 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.440 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 3.0797 time to fit residues: 178.7501 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2619 Z= 0.200 Angle : 0.532 4.281 3534 Z= 0.285 Chirality : 0.051 0.136 420 Planarity : 0.005 0.071 453 Dihedral : 5.977 18.727 357 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.04 % Allowed : 16.84 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.006 0.002 PHE A 378 TYR 0.007 0.001 TYR D 310 ARG 0.012 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: B 372 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6198 (mt-10) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 2.9692 time to fit residues: 172.4963 Evaluate side-chains 57 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2619 Z= 0.160 Angle : 0.518 4.089 3534 Z= 0.275 Chirality : 0.050 0.132 420 Planarity : 0.005 0.077 453 Dihedral : 5.855 19.214 357 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.02 % Allowed : 18.86 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.004 0.001 PHE A 378 TYR 0.006 0.001 TYR E 310 ARG 0.011 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 2.9639 time to fit residues: 157.1170 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2619 Z= 0.212 Angle : 0.549 4.253 3534 Z= 0.293 Chirality : 0.050 0.132 420 Planarity : 0.005 0.077 453 Dihedral : 6.004 18.737 357 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.03 % Allowed : 17.85 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 388 PHE 0.004 0.001 PHE C 378 TYR 0.007 0.001 TYR D 310 ARG 0.013 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.433 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 2.7543 time to fit residues: 151.8436 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 27 optimal weight: 0.0570 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2619 Z= 0.133 Angle : 0.502 4.153 3534 Z= 0.265 Chirality : 0.049 0.130 420 Planarity : 0.005 0.078 453 Dihedral : 5.685 18.620 357 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.69 % Allowed : 17.85 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.003 0.001 PHE C 378 TYR 0.005 0.001 TYR E 310 ARG 0.013 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.545 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 2.8683 time to fit residues: 158.1670 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2619 Z= 0.129 Angle : 0.491 4.075 3534 Z= 0.259 Chirality : 0.049 0.133 420 Planarity : 0.005 0.075 453 Dihedral : 5.521 17.800 357 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.68 % Allowed : 18.18 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.003 0.001 PHE C 378 TYR 0.005 0.001 TYR E 310 ARG 0.015 0.002 ARG C 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 2.8987 time to fit residues: 156.7359 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.128370 restraints weight = 8354.439| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.60 r_work: 0.3971 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2619 Z= 0.116 Angle : 0.485 4.281 3534 Z= 0.254 Chirality : 0.049 0.131 420 Planarity : 0.005 0.075 453 Dihedral : 5.343 17.699 357 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.36 % Allowed : 17.85 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 388 PHE 0.002 0.000 PHE C 378 TYR 0.004 0.001 TYR F 310 ARG 0.014 0.002 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4342.93 seconds wall clock time: 75 minutes 25.78 seconds (4525.78 seconds total)