Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:36:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/11_2022/7qjz_14027.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 2.30, per 1000 atoms: 0.68 Number of scatterers: 3378 At special positions: 0 Unit cell: (122.08, 116.63, 39.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 612 7.00 C 2124 6.00 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: 1.19 Conformation dependent library (CDL) restraints added in 514.2 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 7.040A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.816A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 326 through 330 removed outlier: 7.938A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 362 removed outlier: 9.046A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.479A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.461A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 316 removed outlier: 7.341A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.377A pdb=" N ASN D 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS F 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.984A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 369 through 371 removed outlier: 6.438A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 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: 0.81 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 493 1.45 - 1.57: 2052 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3432 Sorted by residual: bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.03e+00 bond pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta sigma weight residual 1.526 1.553 -0.026 9.30e-03 1.16e+04 8.02e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.69e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.45e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 100.66 - 106.37: 133 106.37 - 112.07: 1417 112.07 - 117.78: 1021 117.78 - 123.48: 1663 123.48 - 129.19: 362 Bond angle restraints: 4596 Sorted by residual: angle pdb=" CA ASN C 327 " pdb=" CB ASN C 327 " pdb=" CG ASN C 327 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.09e+01 angle pdb=" CA LYS C 331 " pdb=" C LYS C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 118.16 122.99 -4.83 7.00e-01 2.04e+00 4.75e+01 angle pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 122.34 -4.18 7.00e-01 2.04e+00 3.56e+01 angle pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " pdb=" CG ASN B 327 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.13e+01 ... (remaining 4591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1888 16.24 - 32.48: 156 32.48 - 48.72: 29 48.72 - 64.96: 5 64.96 - 81.19: 10 Dihedral angle restraints: 2088 sinusoidal: 864 harmonic: 1224 Sorted by residual: dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP E 314 " pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 258 0.062 - 0.124: 161 0.124 - 0.185: 73 0.185 - 0.247: 23 0.247 - 0.309: 7 Chirality restraints: 522 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 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER A 324 " pdb=" N SER A 324 " pdb=" C SER A 324 " pdb=" CB SER A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP D 345 " pdb=" N ASP D 345 " pdb=" C ASP D 345 " pdb=" CB ASP D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 519 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.075 2.00e-02 2.50e+03 5.14e-02 5.29e+01 pdb=" CG TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.084 2.00e-02 2.50e+03 5.11e-02 5.22e+01 pdb=" CG TYR D 310 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 329 " -0.076 2.00e-02 2.50e+03 5.66e-02 4.81e+01 pdb=" CG HIS F 329 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS F 329 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS F 329 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 HIS F 329 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS F 329 " -0.050 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1511 2.97 - 3.45: 2933 3.45 - 3.94: 5105 3.94 - 4.42: 5246 4.42 - 4.90: 10498 Nonbonded interactions: 25293 Sorted by model distance: nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.490 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.509 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.539 2.440 nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.640 2.496 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.643 2.520 ... (remaining 25288 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2124 2.51 5 N 612 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.620 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: 0.010 Extract box with map and model: 3.600 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 0.037 3432 Z= 0.762 Angle : 2.094 10.065 4596 Z= 1.374 Chirality : 0.097 0.309 522 Planarity : 0.013 0.062 582 Dihedral : 13.722 81.195 1308 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.32 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: -3.28 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2213 time to fit residues: 23.4694 Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 307 GLN D 336 GLN D 362 HIS E 307 GLN E 336 GLN E 362 HIS F 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3432 Z= 0.231 Angle : 0.811 6.430 4596 Z= 0.420 Chirality : 0.054 0.141 522 Planarity : 0.004 0.036 582 Dihedral : 7.943 19.580 450 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.82 % 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: -2.96 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.431 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.1737 time to fit residues: 14.9839 Evaluate side-chains 68 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0325 time to fit residues: 1.0473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.051 3432 Z= 0.511 Angle : 0.904 6.285 4596 Z= 0.476 Chirality : 0.056 0.145 522 Planarity : 0.005 0.034 582 Dihedral : 7.689 19.906 450 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 3.33 % 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: -3.43 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.23), residues: 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.446 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.2357 time to fit residues: 23.1227 Evaluate side-chains 75 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0350 time to fit residues: 1.2153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3432 Z= 0.263 Angle : 0.764 7.184 4596 Z= 0.386 Chirality : 0.052 0.140 522 Planarity : 0.003 0.027 582 Dihedral : 6.827 19.552 450 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 1.28 % 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: -3.18 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.418 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.2049 time to fit residues: 17.1351 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0338 time to fit residues: 0.7638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3432 Z= 0.193 Angle : 0.711 10.165 4596 Z= 0.352 Chirality : 0.051 0.133 522 Planarity : 0.003 0.029 582 Dihedral : 6.127 16.679 450 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.03 % 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: -3.07 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.414 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 0.2095 time to fit residues: 16.7267 Evaluate side-chains 62 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0331 time to fit residues: 0.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 0.0470 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3432 Z= 0.212 Angle : 0.686 9.215 4596 Z= 0.341 Chirality : 0.051 0.143 522 Planarity : 0.003 0.031 582 Dihedral : 5.851 15.657 450 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.03 % 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: -3.04 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.398 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.2171 time to fit residues: 15.7665 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0328 time to fit residues: 0.6838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.0970 overall best weight: 2.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3432 Z= 0.191 Angle : 0.675 9.680 4596 Z= 0.331 Chirality : 0.050 0.167 522 Planarity : 0.003 0.031 582 Dihedral : 5.593 14.673 450 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.03 % 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: -3.06 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.25), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.415 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 62 average time/residue: 0.2170 time to fit residues: 15.7395 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0371 time to fit residues: 0.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3432 Z= 0.181 Angle : 0.666 9.291 4596 Z= 0.328 Chirality : 0.050 0.174 522 Planarity : 0.003 0.032 582 Dihedral : 5.387 14.297 450 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.28 % 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: -2.96 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.416 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.2048 time to fit residues: 15.6730 Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0335 time to fit residues: 0.7321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 41 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3432 Z= 0.148 Angle : 0.651 8.728 4596 Z= 0.322 Chirality : 0.049 0.166 522 Planarity : 0.004 0.039 582 Dihedral : 5.128 13.376 450 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.26 % 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: -2.84 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.400 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1959 time to fit residues: 14.9944 Evaluate side-chains 59 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0344 time to fit residues: 0.6574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3432 Z= 0.146 Angle : 0.620 8.394 4596 Z= 0.309 Chirality : 0.049 0.161 522 Planarity : 0.004 0.037 582 Dihedral : 4.890 13.007 450 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.26 % 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: -2.78 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.451 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.2223 time to fit residues: 15.3659 Evaluate side-chains 55 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 20.0000 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** 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 = 0.4246 r_free = 0.4246 target = 0.130921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.111884 restraints weight = 4909.362| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.40 r_work: 0.4012 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work: 0.3998 rms_B_bonded: 2.19 restraints_weight: 0.1250 r_work: 0.3990 rms_B_bonded: 2.23 restraints_weight: 0.0625 r_work: 0.3983 rms_B_bonded: 2.30 restraints_weight: 0.0312 r_work: 0.3975 rms_B_bonded: 2.39 restraints_weight: 0.0156 r_work: 0.3966 rms_B_bonded: 2.50 restraints_weight: 0.0078 r_work: 0.3957 rms_B_bonded: 2.63 restraints_weight: 0.0039 r_work: 0.3947 rms_B_bonded: 2.78 restraints_weight: 0.0020 r_work: 0.3937 rms_B_bonded: 2.95 restraints_weight: 0.0010 r_work: 0.3926 rms_B_bonded: 3.14 restraints_weight: 0.0005 r_work: 0.3915 rms_B_bonded: 3.36 restraints_weight: 0.0002 r_work: 0.3903 rms_B_bonded: 3.61 restraints_weight: 0.0001 r_work: 0.3890 rms_B_bonded: 3.89 restraints_weight: 0.0001 r_work: 0.3876 rms_B_bonded: 4.20 restraints_weight: 0.0000 r_work: 0.3861 rms_B_bonded: 4.55 restraints_weight: 0.0000 r_work: 0.3845 rms_B_bonded: 4.94 restraints_weight: 0.0000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 3432 Z= 0.145 Angle : 0.617 9.447 4596 Z= 0.301 Chirality : 0.048 0.159 522 Planarity : 0.004 0.032 582 Dihedral : 4.729 12.292 450 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.26 % 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: -2.74 (0.36), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 432 =============================================================================== Job complete usr+sys time: 1180.18 seconds wall clock time: 22 minutes 13.44 seconds (1333.44 seconds total)