Starting phenix.real_space_refine on Fri Mar 15 04:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/03_2024/8q8s_18259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/03_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_18259/03_2024/8q8s_18259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/03_2024/8q8s_18259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/03_2024/8q8s_18259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8s_18259/03_2024/8q8s_18259.pdb" } 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-5265/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: 4.96, per 1000 atoms: 0.47 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: 7.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 3.39 Time building geometry restraints manager: 8.12 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 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.558 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.576 1.850 ... (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 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: 3.350 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: 12.360 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.270 Find NCS groups from input model: 0.470 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.270 ------------------------------------------------------------------------------- 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 : 0.849 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: 2.6612 time to fit residues: 548.6700 Evaluate side-chains 112 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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: 8.9990 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: 5.9990 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** F 307 GLN F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5283 Z= 0.284 Angle : 0.781 6.720 7065 Z= 0.427 Chirality : 0.051 0.148 792 Planarity : 0.004 0.038 900 Dihedral : 6.997 27.654 702 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.69 % Allowed : 14.48 % Favored : 82.83 % 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: -2.11 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 362 PHE 0.007 0.001 PHE A 346 TYR 0.011 0.003 TYR D 310 ARG 0.004 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 134 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8508 (mt) cc_final: 0.8167 (mm) REVERT: I 349 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6977 (mtp180) REVERT: I 369 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7694 (mtmm) REVERT: I 375 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7639 (ttmp) REVERT: B 311 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (tmmt) REVERT: B 340 LYS cc_start: 0.7698 (tttm) cc_final: 0.7334 (ttmp) REVERT: B 349 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6854 (mtp180) REVERT: B 351 GLN cc_start: 0.7577 (tt0) cc_final: 0.7290 (mt0) REVERT: D 338 GLU cc_start: 0.6565 (tt0) cc_final: 0.6264 (tt0) REVERT: C 353 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7257 (mmpt) REVERT: C 369 LYS cc_start: 0.7283 (mtpt) cc_final: 0.6954 (mttm) REVERT: E 369 LYS cc_start: 0.7333 (mtpt) cc_final: 0.7085 (mttp) REVERT: F 358 ASP cc_start: 0.6231 (m-30) cc_final: 0.5942 (m-30) REVERT: F 375 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7322 (tptt) REVERT: G 321 LYS cc_start: 0.7706 (mttt) cc_final: 0.7483 (tttt) REVERT: G 369 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6842 (mttm) REVERT: H 315 LEU cc_start: 0.8106 (mt) cc_final: 0.7737 (mt) REVERT: H 369 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7250 (mtpp) REVERT: A 375 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7210 (ttpt) outliers start: 16 outliers final: 5 residues processed: 129 average time/residue: 2.6726 time to fit residues: 357.3605 Evaluate side-chains 107 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 F residue 305 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain G residue 343 LYS 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: 8.9990 chunk 17 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** I 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN C 374 HIS G 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5283 Z= 0.306 Angle : 0.723 6.629 7065 Z= 0.394 Chirality : 0.052 0.149 792 Planarity : 0.005 0.044 900 Dihedral : 6.818 24.380 702 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.04 % Allowed : 15.32 % Favored : 80.64 % 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: -2.58 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 330 PHE 0.010 0.002 PHE D 378 TYR 0.016 0.003 TYR D 310 ARG 0.006 0.001 ARG G 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 125 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8570 (mt) cc_final: 0.8238 (mm) REVERT: I 369 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7724 (mtmm) REVERT: B 349 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6749 (mtp180) REVERT: B 351 GLN cc_start: 0.7565 (tt0) cc_final: 0.7324 (mt0) REVERT: D 311 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7754 (ttpp) REVERT: D 331 LYS cc_start: 0.7921 (mttp) cc_final: 0.7716 (mtpt) REVERT: D 338 GLU cc_start: 0.6674 (tt0) cc_final: 0.6371 (tt0) REVERT: D 370 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7863 (ttmt) REVERT: C 369 LYS cc_start: 0.7377 (mtpt) cc_final: 0.7018 (mttm) REVERT: E 369 LYS cc_start: 0.7337 (mtpt) cc_final: 0.7072 (mttp) REVERT: G 369 LYS cc_start: 0.7252 (mtpt) cc_final: 0.6908 (mttm) REVERT: H 315 LEU cc_start: 0.8156 (mt) cc_final: 0.7800 (mt) REVERT: H 369 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7422 (mtpp) REVERT: A 369 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7113 (mttp) REVERT: A 375 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7252 (ttpt) outliers start: 24 outliers final: 15 residues processed: 116 average time/residue: 2.6742 time to fit residues: 322.0841 Evaluate side-chains 107 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 305 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 353 LYS 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: 0.0980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5283 Z= 0.259 Angle : 0.653 6.532 7065 Z= 0.354 Chirality : 0.050 0.137 792 Planarity : 0.005 0.045 900 Dihedral : 6.616 25.241 702 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.86 % Allowed : 18.18 % Favored : 78.96 % 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: -2.71 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.009 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.002 0.000 ARG A 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 113 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8570 (mt) cc_final: 0.8245 (mm) REVERT: I 349 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6733 (mtp180) REVERT: I 369 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7735 (mtmm) REVERT: B 321 LYS cc_start: 0.8279 (ttmm) cc_final: 0.8056 (ttmm) REVERT: B 351 GLN cc_start: 0.7550 (tt0) cc_final: 0.7342 (mt0) REVERT: D 370 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7791 (ttmt) REVERT: C 369 LYS cc_start: 0.7418 (mtpt) cc_final: 0.7042 (mttm) REVERT: E 369 LYS cc_start: 0.7325 (mtpt) cc_final: 0.7065 (mttp) REVERT: E 379 ARG cc_start: 0.5000 (mtm180) cc_final: 0.4394 (pmt170) REVERT: G 369 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6899 (mttm) REVERT: H 315 LEU cc_start: 0.8195 (mt) cc_final: 0.7820 (mt) REVERT: H 369 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7413 (mtpp) REVERT: A 311 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7731 (mptp) REVERT: A 369 LYS cc_start: 0.7553 (mtpt) cc_final: 0.7149 (mttp) REVERT: A 375 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7262 (ttpt) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 2.6547 time to fit residues: 301.0067 Evaluate side-chains 106 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B 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 305 SER Chi-restraints excluded: chain F residue 311 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 Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5283 Z= 0.296 Angle : 0.678 6.478 7065 Z= 0.364 Chirality : 0.051 0.132 792 Planarity : 0.005 0.056 900 Dihedral : 6.569 22.299 702 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.55 % Allowed : 17.34 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 329 PHE 0.008 0.002 PHE B 378 TYR 0.012 0.003 TYR C 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 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 124 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8541 (mt) cc_final: 0.8218 (mm) REVERT: I 349 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6712 (mtp180) REVERT: B 349 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6579 (mtp180) REVERT: D 370 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7793 (ttmt) REVERT: C 369 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7045 (mttm) REVERT: E 369 LYS cc_start: 0.7352 (mtpt) cc_final: 0.7115 (mttp) REVERT: E 379 ARG cc_start: 0.5047 (mtm180) cc_final: 0.4424 (pmt170) REVERT: F 311 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8037 (mtmm) REVERT: G 349 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7144 (ttp-110) REVERT: G 369 LYS cc_start: 0.7291 (mtpt) cc_final: 0.6948 (mttm) REVERT: H 315 LEU cc_start: 0.8204 (mt) cc_final: 0.7813 (mt) REVERT: H 369 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7452 (mtpp) REVERT: A 331 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7435 (tmtt) REVERT: A 369 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7205 (mttp) REVERT: A 375 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7270 (ttpt) outliers start: 27 outliers final: 14 residues processed: 115 average time/residue: 2.8487 time to fit residues: 339.0504 Evaluate side-chains 110 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5283 Z= 0.409 Angle : 0.745 6.840 7065 Z= 0.400 Chirality : 0.052 0.134 792 Planarity : 0.006 0.060 900 Dihedral : 6.846 24.255 702 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.70 % Allowed : 19.70 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 329 PHE 0.011 0.002 PHE B 378 TYR 0.014 0.003 TYR A 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 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 117 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.854 Fit side-chains REVERT: I 308 ILE cc_start: 0.8555 (mt) cc_final: 0.8230 (mm) REVERT: I 349 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6683 (mtp180) REVERT: B 349 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6484 (mtp180) REVERT: D 370 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (ttmt) REVERT: C 369 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7054 (mttm) REVERT: E 369 LYS cc_start: 0.7351 (mtpt) cc_final: 0.7122 (mttp) REVERT: E 379 ARG cc_start: 0.5075 (mtm180) cc_final: 0.4223 (ptp90) REVERT: F 311 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8099 (mtmm) REVERT: G 369 LYS cc_start: 0.7345 (mtpt) cc_final: 0.6993 (mttm) REVERT: H 369 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7491 (mtpp) REVERT: A 311 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7747 (mptp) REVERT: A 331 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7455 (tmtt) REVERT: A 369 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7166 (mttp) REVERT: A 375 LYS cc_start: 0.7570 (ttmt) cc_final: 0.7289 (ttpt) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 2.8699 time to fit residues: 320.9766 Evaluate side-chains 107 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain B 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5283 Z= 0.173 Angle : 0.591 7.371 7065 Z= 0.314 Chirality : 0.050 0.133 792 Planarity : 0.005 0.055 900 Dihedral : 6.133 24.028 702 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.19 % Allowed : 19.87 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (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 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 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 101 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8563 (mt) cc_final: 0.8238 (mm) REVERT: I 336 GLN cc_start: 0.7115 (mt0) cc_final: 0.6855 (mt0) REVERT: I 349 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6640 (mtp180) REVERT: C 369 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7064 (mttm) REVERT: C 375 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7099 (ttpt) REVERT: E 369 LYS cc_start: 0.7301 (mtpt) cc_final: 0.7070 (mttp) REVERT: E 379 ARG cc_start: 0.4969 (mtm180) cc_final: 0.4441 (pmt170) REVERT: G 369 LYS cc_start: 0.7172 (mtpt) cc_final: 0.6837 (mttm) REVERT: H 369 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7332 (mtpp) REVERT: A 311 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7633 (mptp) REVERT: A 331 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7417 (tmtt) REVERT: A 349 ARG cc_start: 0.5115 (mmp-170) cc_final: 0.4202 (mmm-85) REVERT: A 369 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7173 (mttp) REVERT: A 375 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7235 (ttpp) outliers start: 13 outliers final: 9 residues processed: 97 average time/residue: 2.9556 time to fit residues: 296.7347 Evaluate side-chains 96 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5283 Z= 0.146 Angle : 0.540 7.385 7065 Z= 0.285 Chirality : 0.049 0.133 792 Planarity : 0.005 0.064 900 Dihedral : 5.440 21.190 702 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.68 % Allowed : 20.71 % Favored : 77.61 % 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: -2.71 (0.27), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.013 0.001 PHE A 346 TYR 0.005 0.001 TYR G 310 ARG 0.015 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 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 109 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8577 (mt) cc_final: 0.8248 (mm) REVERT: I 349 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6581 (mtp180) REVERT: B 336 GLN cc_start: 0.7464 (mt0) cc_final: 0.7170 (mt0) REVERT: C 369 LYS cc_start: 0.7457 (mtpt) cc_final: 0.7057 (mttm) REVERT: C 375 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7052 (ttpt) REVERT: E 369 LYS cc_start: 0.7252 (mtpt) cc_final: 0.7008 (mttp) REVERT: E 379 ARG cc_start: 0.4994 (mtm180) cc_final: 0.4453 (pmt170) REVERT: G 327 ASN cc_start: 0.8485 (t0) cc_final: 0.8281 (t0) REVERT: G 369 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6787 (mttm) REVERT: H 369 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7283 (mtpp) REVERT: A 311 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7591 (mptp) REVERT: A 331 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7432 (tmtt) REVERT: A 369 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7205 (mttp) REVERT: A 375 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7241 (ttpp) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 2.5608 time to fit residues: 282.3709 Evaluate side-chains 97 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5283 Z= 0.175 Angle : 0.566 7.609 7065 Z= 0.299 Chirality : 0.049 0.128 792 Planarity : 0.005 0.054 900 Dihedral : 5.516 19.909 702 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.68 % Allowed : 21.04 % Favored : 77.27 % 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: -2.69 (0.27), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.008 0.001 PHE D 378 TYR 0.007 0.002 TYR G 310 ARG 0.012 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 9 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 97 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8565 (mt) cc_final: 0.8243 (mm) REVERT: I 349 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6571 (mtp180) REVERT: C 369 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7054 (mttm) REVERT: C 375 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7037 (ttpt) REVERT: E 369 LYS cc_start: 0.7262 (mtpt) cc_final: 0.7024 (mttp) REVERT: E 379 ARG cc_start: 0.4990 (mtm180) cc_final: 0.4448 (pmt170) REVERT: G 343 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7425 (ptmt) REVERT: G 369 LYS cc_start: 0.7165 (mtpt) cc_final: 0.6827 (mttm) REVERT: H 369 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7383 (mtpp) REVERT: A 311 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7621 (mptp) REVERT: A 331 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7442 (tmtt) REVERT: A 349 ARG cc_start: 0.4868 (mmp-170) cc_final: 0.4127 (mmm-85) REVERT: A 369 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7252 (mttp) REVERT: A 375 LYS cc_start: 0.7533 (ttmt) cc_final: 0.7257 (ttpp) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 2.7610 time to fit residues: 269.3019 Evaluate side-chains 95 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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: 0.7497 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5283 Z= 0.267 Angle : 0.634 7.523 7065 Z= 0.336 Chirality : 0.050 0.129 792 Planarity : 0.006 0.061 900 Dihedral : 5.965 22.834 702 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.68 % Allowed : 21.72 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.27), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 329 PHE 0.008 0.002 PHE D 378 TYR 0.010 0.002 TYR G 310 ARG 0.012 0.001 ARG G 349 ********************** REFINEMENT MACRO_CYCLE 10 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 94 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.931 Fit side-chains REVERT: I 308 ILE cc_start: 0.8566 (mt) cc_final: 0.8240 (mm) REVERT: I 349 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6599 (mtp180) REVERT: D 370 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: C 369 LYS cc_start: 0.7472 (mtpt) cc_final: 0.7062 (mttm) REVERT: E 369 LYS cc_start: 0.7340 (mtpt) cc_final: 0.7105 (mttp) REVERT: E 379 ARG cc_start: 0.4999 (mtm180) cc_final: 0.4239 (ptp90) REVERT: G 369 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6882 (mttm) REVERT: H 369 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7420 (mtpp) REVERT: A 311 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7657 (mptp) REVERT: A 331 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7436 (tmtt) REVERT: A 369 LYS cc_start: 0.7536 (mtpt) cc_final: 0.7111 (mttp) REVERT: A 375 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7302 (ttpt) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 2.7853 time to fit residues: 266.1264 Evaluate side-chains 91 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.170554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.148229 restraints weight = 17270.801| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 1.88 r_work: 0.4178 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4088 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5283 Z= 0.181 Angle : 0.591 7.730 7065 Z= 0.312 Chirality : 0.050 0.127 792 Planarity : 0.005 0.061 900 Dihedral : 5.830 24.036 702 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.35 % Allowed : 22.56 % Favored : 76.09 % 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: -2.75 (0.27), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.008 0.001 PHE D 378 TYR 0.008 0.001 TYR G 310 ARG 0.012 0.001 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5878.12 seconds wall clock time: 102 minutes 41.82 seconds (6161.82 seconds total)