Starting phenix.real_space_refine on Sun Aug 4 13:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/08_2024/8q8s_18259.cif" } resolution = 2.68 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 9 5.16 5 C 3258 2.51 5 N 963 2.21 5 O 972 1.98 5 H 5409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 342": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" 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: 10611 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 6.06, per 1000 atoms: 0.57 Number of scatterers: 10611 At special positions: 0 Unit cell: (142.492, 136.676, 44.347, 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 9 16.00 O 972 8.00 N 963 7.00 C 3258 6.00 H 5409 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: 7.51 Conformation dependent library (CDL) restraints added in 988.6 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.705A pdb=" N VAL I 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 317 through 321 Processing sheet with id=AA4, first strand: chain 'I' and resid 325 through 330 removed outlier: 7.061A pdb=" N GLY D 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN I 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 337 through 340 removed outlier: 6.552A pdb=" N GLU I 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.450A pdb=" N GLN I 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE D 354 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS I 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 357 through 362 removed outlier: 6.634A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.493A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 374 through 378 removed outlier: 6.613A pdb=" N LYS I 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE D 378 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR I 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.834A pdb=" N VAL C 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.506A pdb=" N LYS C 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER G 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL E 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYS G 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER E 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 7.007A pdb=" N GLY G 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY E 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS G 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.568A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS G 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.581A pdb=" N GLN C 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE G 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS C 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.522A pdb=" N LEU E 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE G 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.523A pdb=" N LYS E 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.553A pdb=" N LYS C 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE G 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR C 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 307 through 310 Processing sheet with id=AC2, first strand: chain 'F' and resid 313 through 314 Processing sheet with id=AC3, first strand: chain 'F' and resid 317 through 322 removed outlier: 6.494A pdb=" N VAL H 318 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LYS A 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER H 320 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 325 through 330 removed outlier: 5.959A pdb=" N GLY F 326 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS H 329 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE F 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY H 326 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N HIS A 329 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE H 328 " --> pdb=" O HIS A 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 337 through 340 removed outlier: 6.610A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 351 through 354 Processing sheet with id=AC7, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.558A pdb=" N LEU F 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE H 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 357 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE A 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN H 359 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS A 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR H 361 " --> pdb=" O HIS A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 369 through 371 removed outlier: 6.506A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS H 370 " --> pdb=" O ILE A 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 374 through 378 removed outlier: 6.497A pdb=" N HIS H 374 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR A 377 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU H 376 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 345 through 346 85 hydrogen bonds defined for protein. 255 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: 3.33 Time building geometry restraints manager: 7.98 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: 5400 1.12 - 1.29: 864 1.29 - 1.47: 1676 1.47 - 1.64: 2743 1.64 - 1.81: 9 Bond restraints: 10692 Sorted by residual: bond pdb=" N SER D 324 " pdb=" H SER D 324 " 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 D 323 " pdb=" H GLY D 323 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL B 363 " pdb=" H VAL B 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL D 363 " pdb=" H VAL D 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL I 363 " pdb=" H VAL I 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.19: 125 104.19 - 111.70: 12182 111.70 - 119.21: 3783 119.21 - 126.72: 3283 126.72 - 134.23: 103 Bond angle restraints: 19476 Sorted by residual: angle pdb=" N ASP H 348 " pdb=" CA ASP H 348 " pdb=" C ASP H 348 " ideal model delta sigma weight residual 110.23 120.21 -9.98 1.45e+00 4.76e-01 4.73e+01 angle pdb=" N SER F 341 " pdb=" CA SER F 341 " pdb=" C SER F 341 " ideal model delta sigma weight residual 108.45 116.16 -7.71 1.26e+00 6.30e-01 3.74e+01 angle pdb=" C SER F 341 " pdb=" N GLU F 342 " pdb=" CA GLU F 342 " ideal model delta sigma weight residual 123.27 134.23 -10.96 1.85e+00 2.92e-01 3.51e+01 angle pdb=" N GLN E 336 " pdb=" CA GLN E 336 " pdb=" C GLN E 336 " ideal model delta sigma weight residual 110.32 119.44 -9.12 1.59e+00 3.96e-01 3.29e+01 angle pdb=" N LYS C 343 " pdb=" CA LYS C 343 " pdb=" C LYS C 343 " ideal model delta sigma weight residual 110.23 118.15 -7.92 1.45e+00 4.76e-01 2.99e+01 ... (remaining 19471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4416 15.94 - 31.87: 227 31.87 - 47.81: 114 47.81 - 63.74: 130 63.74 - 79.67: 36 Dihedral angle restraints: 4923 sinusoidal: 2817 harmonic: 2106 Sorted by residual: dihedral pdb=" CA GLU A 342 " pdb=" C GLU A 342 " pdb=" N LYS A 343 " pdb=" CA LYS A 343 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 459 0.076 - 0.151: 260 0.151 - 0.226: 45 0.226 - 0.302: 19 0.302 - 0.377: 9 Chirality restraints: 792 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ARG I 349 " pdb=" N ARG I 349 " pdb=" C ARG I 349 " pdb=" CB ARG I 349 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 789 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 336 " -0.070 2.00e-02 2.50e+03 6.38e-02 6.10e+01 pdb=" CD GLN H 336 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN H 336 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN H 336 " 0.049 2.00e-02 2.50e+03 pdb="HE21 GLN H 336 " 0.055 2.00e-02 2.50e+03 pdb="HE22 GLN H 336 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 368 " -0.058 2.00e-02 2.50e+03 5.56e-02 4.64e+01 pdb=" CG ASN D 368 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN D 368 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 368 " 0.069 2.00e-02 2.50e+03 pdb="HD21 ASN D 368 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN D 368 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " 0.080 2.00e-02 2.50e+03 3.55e-02 3.79e+01 pdb=" CG TYR H 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " 0.026 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 730 2.16 - 2.77: 17642 2.77 - 3.38: 28361 3.38 - 3.99: 36626 3.99 - 4.60: 52989 Nonbonded interactions: 136348 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.555 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.576 2.450 ... (remaining 136343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.180 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 0.038 5283 Z= 0.774 Angle : 2.114 10.964 7065 Z= 1.379 Chirality : 0.099 0.377 792 Planarity : 0.011 0.087 900 Dihedral : 9.516 77.054 2025 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.51 % 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: -1.68 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.005 HIS B 330 PHE 0.056 0.012 PHE F 378 TYR 0.077 0.023 TYR D 310 ARG 0.006 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 369 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7613 (mtmm) REVERT: I 375 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7478 (ttpp) REVERT: D 321 LYS cc_start: 0.7539 (mttt) cc_final: 0.7286 (ttmm) REVERT: D 338 GLU cc_start: 0.6586 (tt0) cc_final: 0.6254 (tt0) REVERT: D 358 ASP cc_start: 0.7678 (m-30) cc_final: 0.7434 (m-30) REVERT: C 353 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7253 (mmpt) REVERT: C 369 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6961 (mttm) REVERT: E 369 LYS cc_start: 0.7279 (mtpt) cc_final: 0.7026 (mttp) REVERT: F 321 LYS cc_start: 0.7867 (mttt) cc_final: 0.7559 (ttmm) REVERT: F 375 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7174 (tttt) REVERT: G 321 LYS cc_start: 0.7686 (mttt) cc_final: 0.7444 (mttt) REVERT: G 369 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6727 (mttm) REVERT: H 315 LEU cc_start: 0.8046 (mt) cc_final: 0.7779 (mt) REVERT: H 321 LYS cc_start: 0.7834 (mttt) cc_final: 0.7409 (mttm) REVERT: H 344 LEU cc_start: 0.6579 (mt) cc_final: 0.6331 (mp) REVERT: H 369 LYS cc_start: 0.7471 (mtpt) cc_final: 0.7185 (mtpp) REVERT: A 331 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7438 (tmtt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 2.6419 time to fit residues: 544.7720 Evaluate side-chains 112 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN D 368 ASN D 374 HIS F 307 GLN F 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5283 Z= 0.306 Angle : 0.743 6.445 7065 Z= 0.401 Chirality : 0.050 0.151 792 Planarity : 0.004 0.035 900 Dihedral : 7.157 28.141 702 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.53 % Allowed : 14.31 % Favored : 83.16 % 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: -2.20 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 374 PHE 0.007 0.002 PHE B 346 TYR 0.011 0.003 TYR D 310 ARG 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8517 (mt) cc_final: 0.8174 (mm) REVERT: I 349 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6989 (mtp180) REVERT: I 369 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7718 (mtmm) REVERT: I 375 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7714 (ttmp) REVERT: B 311 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7818 (tmmt) REVERT: B 340 LYS cc_start: 0.7660 (tttm) cc_final: 0.7291 (ttmp) REVERT: B 349 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6838 (mtp180) REVERT: B 351 GLN cc_start: 0.7586 (tt0) cc_final: 0.7293 (mt0) REVERT: D 338 GLU cc_start: 0.6624 (tt0) cc_final: 0.6330 (tt0) REVERT: C 353 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7264 (mmtt) REVERT: C 369 LYS cc_start: 0.7365 (mtpt) cc_final: 0.7023 (mttm) REVERT: E 369 LYS cc_start: 0.7310 (mtpt) cc_final: 0.7050 (mttp) REVERT: F 375 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7358 (tptt) REVERT: G 321 LYS cc_start: 0.7729 (mttt) cc_final: 0.7501 (tttt) REVERT: G 369 LYS cc_start: 0.7239 (mtpt) cc_final: 0.6943 (mttm) REVERT: H 315 LEU cc_start: 0.8096 (mt) cc_final: 0.7700 (mt) REVERT: H 369 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7310 (mtpp) REVERT: A 369 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7264 (mttp) REVERT: A 375 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7276 (ttpt) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 2.8264 time to fit residues: 378.1809 Evaluate side-chains 103 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5283 Z= 0.354 Angle : 0.756 6.697 7065 Z= 0.412 Chirality : 0.053 0.153 792 Planarity : 0.005 0.046 900 Dihedral : 6.907 22.458 702 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.87 % Allowed : 15.99 % 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: -2.80 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 330 PHE 0.009 0.002 PHE C 378 TYR 0.018 0.004 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8573 (mt) cc_final: 0.8243 (mm) REVERT: I 349 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6926 (mtp180) REVERT: I 369 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7733 (mtmm) REVERT: I 375 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7751 (ttmp) REVERT: B 340 LYS cc_start: 0.7721 (tttm) cc_final: 0.7330 (ttmp) REVERT: B 342 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: B 349 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6733 (mtp180) REVERT: B 351 GLN cc_start: 0.7603 (tt0) cc_final: 0.7336 (mt0) REVERT: D 311 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7733 (ttpp) REVERT: D 331 LYS cc_start: 0.7935 (mttp) cc_final: 0.7729 (mtpt) REVERT: D 338 GLU cc_start: 0.6702 (tt0) cc_final: 0.6398 (tt0) REVERT: D 370 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7869 (ttmt) REVERT: C 369 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7103 (mttm) REVERT: E 369 LYS cc_start: 0.7348 (mtpt) cc_final: 0.7084 (mttp) REVERT: F 375 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7310 (tptm) REVERT: G 316 SER cc_start: 0.8298 (p) cc_final: 0.8029 (t) REVERT: G 369 LYS cc_start: 0.7313 (mtpt) cc_final: 0.6978 (mttm) REVERT: H 315 LEU cc_start: 0.8115 (mt) cc_final: 0.7706 (mt) REVERT: H 369 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7452 (mtpp) REVERT: A 369 LYS cc_start: 0.7586 (mtpt) cc_final: 0.7281 (mttp) REVERT: A 375 LYS cc_start: 0.7556 (ttmt) cc_final: 0.7325 (ttpt) outliers start: 23 outliers final: 11 residues processed: 119 average time/residue: 2.9525 time to fit residues: 363.5844 Evaluate side-chains 104 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5283 Z= 0.155 Angle : 0.583 6.889 7065 Z= 0.314 Chirality : 0.050 0.133 792 Planarity : 0.004 0.040 900 Dihedral : 6.260 22.430 702 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.68 % Allowed : 18.52 % 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: -2.65 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 330 PHE 0.007 0.001 PHE B 378 TYR 0.006 0.001 TYR G 310 ARG 0.008 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8565 (mt) cc_final: 0.8229 (mm) REVERT: I 349 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6706 (mtp180) REVERT: I 369 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7710 (mtmm) REVERT: I 375 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7742 (ttmp) REVERT: B 321 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7986 (ttmm) REVERT: B 351 GLN cc_start: 0.7521 (tt0) cc_final: 0.7291 (mt0) REVERT: D 370 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7701 (ttmt) REVERT: C 369 LYS cc_start: 0.7500 (mtpt) cc_final: 0.7120 (mttm) REVERT: E 369 LYS cc_start: 0.7198 (mtpt) cc_final: 0.6937 (mttp) REVERT: E 379 ARG cc_start: 0.5061 (mtm180) cc_final: 0.4511 (pmt170) REVERT: F 375 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7306 (tptm) REVERT: G 316 SER cc_start: 0.8165 (p) cc_final: 0.7933 (t) REVERT: G 369 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6920 (mttm) REVERT: H 315 LEU cc_start: 0.8103 (mt) cc_final: 0.7637 (mt) REVERT: H 369 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7310 (mtpp) REVERT: A 331 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7413 (tmtt) REVERT: A 369 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7270 (mttp) REVERT: A 375 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7330 (ttpt) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 2.6343 time to fit residues: 292.7835 Evaluate side-chains 98 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2217 > 50: distance: 72 - 460: 28.184 distance: 75 - 488: 9.533 distance: 103 - 491: 15.229 distance: 410 - 419: 23.197 distance: 419 - 420: 11.014 distance: 419 - 423: 17.292 distance: 420 - 421: 18.412 distance: 420 - 424: 16.216 distance: 420 - 425: 13.162 distance: 421 - 422: 25.439 distance: 421 - 426: 41.754 distance: 426 - 427: 6.699 distance: 426 - 430: 22.805 distance: 427 - 428: 23.917 distance: 427 - 431: 15.108 distance: 427 - 432: 13.041 distance: 428 - 429: 8.354 distance: 428 - 433: 9.079 distance: 433 - 434: 27.123 distance: 433 - 437: 24.225 distance: 434 - 435: 32.586 distance: 434 - 438: 12.838 distance: 434 - 439: 19.247 distance: 435 - 436: 47.792 distance: 435 - 440: 40.979 distance: 440 - 441: 8.509 distance: 440 - 449: 20.806 distance: 441 - 442: 14.058 distance: 441 - 444: 9.396 distance: 441 - 450: 8.205 distance: 442 - 443: 13.050 distance: 442 - 457: 14.808 distance: 444 - 445: 7.767 distance: 444 - 452: 5.166 distance: 457 - 458: 13.419 distance: 457 - 464: 6.586 distance: 458 - 459: 20.127 distance: 458 - 461: 8.043 distance: 458 - 465: 6.512 distance: 459 - 460: 29.512 distance: 459 - 473: 33.142 distance: 461 - 462: 3.198 distance: 461 - 466: 3.456 distance: 462 - 468: 3.266 distance: 462 - 469: 3.650 distance: 463 - 472: 3.388 distance: 473 - 474: 7.359 distance: 473 - 482: 22.383 distance: 474 - 475: 4.901 distance: 474 - 477: 4.922 distance: 474 - 483: 6.715 distance: 475 - 476: 15.459 distance: 475 - 488: 17.447 distance: 477 - 478: 6.829 distance: 477 - 484: 3.111 distance: 478 - 487: 4.732 distance: 488 - 489: 12.909 distance: 488 - 495: 15.615 distance: 489 - 490: 23.099 distance: 489 - 492: 12.480 distance: 489 - 496: 4.316 distance: 490 - 491: 19.440 distance: 490 - 504: 31.987 distance: 492 - 493: 4.496 distance: 492 - 494: 3.631 distance: 492 - 497: 3.402 distance: 493 - 500: 4.732 distance: 494 - 501: 3.161 distance: 494 - 502: 4.967 distance: 494 - 503: 3.290 distance: 504 - 505: 15.750 distance: 504 - 513: 16.981 distance: 505 - 506: 16.091 distance: 505 - 508: 10.204 distance: 505 - 514: 7.137 distance: 506 - 507: 15.833 distance: 506 - 526: 14.282 distance: 526 - 527: 21.597 distance: 526 - 532: 9.036 distance: 527 - 528: 19.907 distance: 527 - 530: 15.734 distance: 527 - 533: 17.802 distance: 528 - 529: 10.761 distance: 528 - 537: 11.246 distance: 530 - 531: 7.782 distance: 531 - 536: 8.192 distance: 537 - 538: 19.069 distance: 537 - 546: 5.642 distance: 538 - 539: 17.525 distance: 538 - 541: 12.945 distance: 538 - 547: 11.687 distance: 539 - 540: 13.853 distance: 539 - 552: 17.042 distance: 541 - 542: 3.602 distance: 541 - 548: 3.285 distance: 542 - 543: 3.605