Starting phenix.real_space_refine on Fri Aug 2 14:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9erm_19926/08_2024/9erm_19926.cif" } resolution = 2.3 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.69, per 1000 atoms: 0.94 Number of scatterers: 2870 At special positions: 0 Unit cell: (105.472, 123.6, 32.96, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 0.71 Conformation dependent library (CDL) restraints added in 448.4 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.557A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.437A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.843A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 8.960A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU A 338 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A 340 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER D 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 342 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.431A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.472A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.365A pdb=" N LYS A 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR D 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS D 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS A 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR D 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.437A pdb=" N VAL B 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LYS E 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER B 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.128A pdb=" N GLY B 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N HIS E 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.991A pdb=" N GLU B 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL E 339 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER E 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU B 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.472A pdb=" N THR B 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.365A pdb=" N LYS B 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS E 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS B 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR E 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 49 hydrogen bonds defined for protein. 147 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: 0.61 Time building geometry restraints manager: 0.83 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: 641 1.33 - 1.45: 563 1.45 - 1.57: 1706 1.57 - 1.69: 0 1.69 - 1.80: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" C GLY E 355 " pdb=" O GLY E 355 " ideal model delta sigma weight residual 1.236 1.223 0.013 5.30e-03 3.56e+04 5.60e+00 bond pdb=" C GLY A 355 " pdb=" O GLY A 355 " ideal model delta sigma weight residual 1.236 1.223 0.012 5.30e-03 3.56e+04 5.56e+00 bond pdb=" C GLY B 355 " pdb=" O GLY B 355 " ideal model delta sigma weight residual 1.236 1.223 0.012 5.30e-03 3.56e+04 5.51e+00 bond pdb=" C GLY C 355 " pdb=" O GLY C 355 " ideal model delta sigma weight residual 1.236 1.224 0.012 5.30e-03 3.56e+04 5.44e+00 bond pdb=" C GLY D 355 " pdb=" O GLY D 355 " ideal model delta sigma weight residual 1.236 1.224 0.012 5.30e-03 3.56e+04 5.42e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 103.39 - 109.15: 456 109.15 - 114.92: 1404 114.92 - 120.68: 1096 120.68 - 126.45: 909 126.45 - 132.21: 35 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C LEU E 376 " pdb=" CA LEU E 376 " pdb=" CB LEU E 376 " ideal model delta sigma weight residual 110.14 117.52 -7.38 1.60e+00 3.91e-01 2.13e+01 angle pdb=" C LEU D 376 " pdb=" CA LEU D 376 " pdb=" CB LEU D 376 " ideal model delta sigma weight residual 110.14 117.51 -7.37 1.60e+00 3.91e-01 2.12e+01 angle pdb=" C LEU A 376 " pdb=" CA LEU A 376 " pdb=" CB LEU A 376 " ideal model delta sigma weight residual 110.14 117.49 -7.35 1.60e+00 3.91e-01 2.11e+01 angle pdb=" C LEU B 376 " pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " ideal model delta sigma weight residual 110.14 117.47 -7.33 1.60e+00 3.91e-01 2.10e+01 angle pdb=" C LEU C 376 " pdb=" CA LEU C 376 " pdb=" CB LEU C 376 " ideal model delta sigma weight residual 110.14 117.46 -7.32 1.60e+00 3.91e-01 2.09e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.64: 1510 10.64 - 21.28: 210 21.28 - 31.92: 40 31.92 - 42.56: 5 42.56 - 53.20: 15 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 170 0.056 - 0.111: 206 0.111 - 0.167: 45 0.167 - 0.223: 14 0.223 - 0.278: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LYS E 317 " pdb=" N LYS E 317 " pdb=" C LYS E 317 " pdb=" CB LYS E 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 370 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C LYS C 370 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS C 370 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 370 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C LYS A 370 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A 370 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 370 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C LYS D 370 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS D 370 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE D 371 " 0.010 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1721 3.09 - 3.54: 2610 3.54 - 4.00: 4102 4.00 - 4.45: 4278 4.45 - 4.90: 8165 Nonbonded interactions: 20876 Sorted by model distance: nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.641 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.642 2.496 ... (remaining 20871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.570 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 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 : 0.009 0.055 2915 Z= 0.634 Angle : 1.427 7.377 3900 Z= 0.908 Chirality : 0.088 0.278 440 Planarity : 0.010 0.056 495 Dihedral : 11.153 53.196 1120 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.03 % Allowed : 6.06 % Favored : 90.91 % 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: -2.04 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 374 PHE 0.007 0.002 PHE D 378 TYR 0.012 0.006 TYR E 310 ARG 0.010 0.003 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.356 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: A 307 GLN cc_start: 0.8336 (mt0) cc_final: 0.7876 (tt0) REVERT: A 317 LYS cc_start: 0.8806 (pttt) cc_final: 0.8524 (ptpp) REVERT: A 331 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8832 (mtpp) REVERT: A 340 LYS cc_start: 0.8874 (mtpm) cc_final: 0.8290 (mttm) REVERT: A 376 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 307 GLN cc_start: 0.8600 (mt0) cc_final: 0.8196 (tt0) REVERT: B 317 LYS cc_start: 0.8897 (pttt) cc_final: 0.8634 (ptpp) REVERT: B 331 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8949 (mtpp) REVERT: C 307 GLN cc_start: 0.8628 (mt0) cc_final: 0.8194 (tt0) REVERT: C 317 LYS cc_start: 0.8902 (pttt) cc_final: 0.8626 (ptpp) REVERT: C 331 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8950 (mtpp) REVERT: C 376 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 311 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8323 (mttt) REVERT: D 317 LYS cc_start: 0.8846 (pttt) cc_final: 0.8508 (ptpt) REVERT: D 331 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8826 (mtpp) REVERT: D 376 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8819 (tp) REVERT: E 307 GLN cc_start: 0.8403 (mt0) cc_final: 0.7944 (tt0) REVERT: E 311 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8426 (mttt) REVERT: E 317 LYS cc_start: 0.8817 (pttt) cc_final: 0.8479 (ptpt) REVERT: E 331 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8864 (mtpp) REVERT: E 376 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8852 (tp) outliers start: 10 outliers final: 1 residues processed: 152 average time/residue: 1.4201 time to fit residues: 219.7055 Evaluate side-chains 132 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN B 327 ASN B 336 GLN C 327 ASN C 336 GLN D 327 ASN D 336 GLN E 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2915 Z= 0.162 Angle : 0.592 5.770 3900 Z= 0.293 Chirality : 0.050 0.134 440 Planarity : 0.003 0.018 495 Dihedral : 6.122 35.247 395 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.24 % Allowed : 13.64 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE C 378 TYR 0.003 0.001 TYR B 310 ARG 0.003 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8243 (mt0) cc_final: 0.7986 (tt0) REVERT: A 317 LYS cc_start: 0.8702 (pttt) cc_final: 0.8452 (ptpp) REVERT: A 331 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8824 (mtpp) REVERT: A 340 LYS cc_start: 0.8810 (mtpm) cc_final: 0.8199 (mttm) REVERT: B 307 GLN cc_start: 0.8539 (mt0) cc_final: 0.8256 (tt0) REVERT: B 317 LYS cc_start: 0.8779 (pttt) cc_final: 0.8531 (ptpp) REVERT: B 331 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8969 (mtpp) REVERT: C 307 GLN cc_start: 0.8495 (mt0) cc_final: 0.8173 (tt0) REVERT: C 317 LYS cc_start: 0.8788 (pttt) cc_final: 0.8554 (ptpp) REVERT: C 331 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8948 (mtpp) REVERT: D 317 LYS cc_start: 0.8744 (pttt) cc_final: 0.8480 (ptpt) REVERT: D 331 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8832 (mtpp) REVERT: E 307 GLN cc_start: 0.8078 (mt0) cc_final: 0.7759 (tt0) REVERT: E 311 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8518 (mttt) REVERT: E 317 LYS cc_start: 0.8773 (pttt) cc_final: 0.8479 (ptpt) REVERT: E 331 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8898 (mtpp) REVERT: E 340 LYS cc_start: 0.8813 (mtpm) cc_final: 0.8266 (mttm) outliers start: 14 outliers final: 0 residues processed: 133 average time/residue: 1.4785 time to fit residues: 200.0262 Evaluate side-chains 120 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS B 336 GLN C 336 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2915 Z= 0.467 Angle : 0.776 7.065 3900 Z= 0.380 Chirality : 0.054 0.146 440 Planarity : 0.003 0.021 495 Dihedral : 5.275 16.792 385 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 17.88 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 374 PHE 0.006 0.001 PHE C 378 TYR 0.007 0.002 TYR B 310 ARG 0.004 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8226 (mt0) cc_final: 0.8019 (tt0) REVERT: A 317 LYS cc_start: 0.8757 (pttt) cc_final: 0.8475 (ptpp) REVERT: A 331 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8874 (mtpp) REVERT: A 340 LYS cc_start: 0.8843 (mtpm) cc_final: 0.8221 (mttm) REVERT: B 307 GLN cc_start: 0.8535 (mt0) cc_final: 0.8276 (tt0) REVERT: B 317 LYS cc_start: 0.8874 (pttt) cc_final: 0.8614 (ptpp) REVERT: B 325 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9089 (tt) REVERT: B 331 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8981 (mtpp) REVERT: C 307 GLN cc_start: 0.8533 (mt0) cc_final: 0.8276 (tt0) REVERT: C 317 LYS cc_start: 0.8848 (pttt) cc_final: 0.8622 (ptpp) REVERT: C 325 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8993 (tt) REVERT: C 331 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8961 (mtpp) REVERT: D 317 LYS cc_start: 0.8821 (pttt) cc_final: 0.8521 (ptpt) REVERT: D 331 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8879 (mtpp) REVERT: E 307 GLN cc_start: 0.8148 (mt0) cc_final: 0.7861 (tt0) REVERT: E 311 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8563 (mttt) REVERT: E 317 LYS cc_start: 0.8818 (pttt) cc_final: 0.8447 (ptpt) REVERT: E 331 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8907 (mtpp) REVERT: E 340 LYS cc_start: 0.8844 (mtpm) cc_final: 0.8296 (mttm) outliers start: 14 outliers final: 2 residues processed: 125 average time/residue: 1.6790 time to fit residues: 213.1867 Evaluate side-chains 121 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2915 Z= 0.221 Angle : 0.624 7.588 3900 Z= 0.297 Chirality : 0.049 0.131 440 Planarity : 0.002 0.015 495 Dihedral : 4.924 16.712 385 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 20.00 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.003 0.001 PHE B 378 TYR 0.005 0.001 TYR B 310 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8703 (pttt) cc_final: 0.8438 (ptpp) REVERT: A 331 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8886 (mtpp) REVERT: B 307 GLN cc_start: 0.8515 (mt0) cc_final: 0.8306 (tt0) REVERT: B 317 LYS cc_start: 0.8770 (pttt) cc_final: 0.8507 (ptpp) REVERT: B 331 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8983 (mtpp) REVERT: B 379 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7573 (mtt90) REVERT: C 317 LYS cc_start: 0.8820 (pttt) cc_final: 0.8591 (ptpp) REVERT: C 325 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8951 (tt) REVERT: C 331 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8959 (mtpp) REVERT: D 317 LYS cc_start: 0.8774 (pttt) cc_final: 0.8475 (ptpt) REVERT: D 331 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8849 (mtpp) REVERT: E 307 GLN cc_start: 0.8108 (mt0) cc_final: 0.7846 (tt0) REVERT: E 311 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8532 (mttt) REVERT: E 317 LYS cc_start: 0.8785 (pttt) cc_final: 0.8408 (ptpt) REVERT: E 331 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8894 (mtpp) REVERT: E 340 LYS cc_start: 0.8832 (mtpm) cc_final: 0.8281 (mttm) outliers start: 8 outliers final: 1 residues processed: 123 average time/residue: 1.7230 time to fit residues: 215.1945 Evaluate side-chains 117 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2915 Z= 0.190 Angle : 0.606 8.098 3900 Z= 0.284 Chirality : 0.049 0.128 440 Planarity : 0.002 0.025 495 Dihedral : 4.709 16.401 385 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 20.91 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.002 0.001 PHE B 378 TYR 0.006 0.001 TYR A 310 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8675 (pttt) cc_final: 0.8411 (ptpp) REVERT: A 331 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8888 (mtpp) REVERT: A 340 LYS cc_start: 0.8738 (mtpm) cc_final: 0.8107 (mttm) REVERT: B 317 LYS cc_start: 0.8727 (pttt) cc_final: 0.8470 (ptpp) REVERT: B 331 LYS cc_start: 0.9235 (mtmt) cc_final: 0.8978 (mtpp) REVERT: B 379 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: C 317 LYS cc_start: 0.8821 (pttt) cc_final: 0.8600 (ptpp) REVERT: C 325 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8941 (tt) REVERT: C 331 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8958 (mtpp) REVERT: D 317 LYS cc_start: 0.8765 (pttt) cc_final: 0.8462 (ptpt) REVERT: D 331 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8860 (mtpp) REVERT: E 311 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8527 (mttt) REVERT: E 317 LYS cc_start: 0.8749 (pttt) cc_final: 0.8425 (ptpt) REVERT: E 331 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8892 (mtpp) REVERT: E 340 LYS cc_start: 0.8820 (mtpm) cc_final: 0.8267 (mttm) outliers start: 8 outliers final: 2 residues processed: 119 average time/residue: 1.6959 time to fit residues: 204.9636 Evaluate side-chains 119 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2915 Z= 0.386 Angle : 0.703 7.729 3900 Z= 0.344 Chirality : 0.052 0.140 440 Planarity : 0.003 0.018 495 Dihedral : 5.068 16.845 385 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.42 % Allowed : 20.30 % 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: -1.33 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.005 0.001 PHE C 378 TYR 0.009 0.002 TYR B 310 ARG 0.005 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8692 (pttt) cc_final: 0.8406 (ptpp) REVERT: A 331 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8893 (mtpp) REVERT: A 340 LYS cc_start: 0.8798 (mtpm) cc_final: 0.8154 (mttm) REVERT: B 317 LYS cc_start: 0.8794 (pttt) cc_final: 0.8533 (ptpp) REVERT: B 325 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9087 (tt) REVERT: B 331 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8995 (mtpp) REVERT: C 317 LYS cc_start: 0.8836 (pttt) cc_final: 0.8614 (ptpp) REVERT: C 325 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8969 (tt) REVERT: C 331 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8986 (mtpp) REVERT: C 379 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7290 (mtt90) REVERT: D 317 LYS cc_start: 0.8800 (pttt) cc_final: 0.8502 (ptpt) REVERT: D 331 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8880 (mtpp) REVERT: E 311 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8558 (mttt) REVERT: E 317 LYS cc_start: 0.8787 (pttt) cc_final: 0.8396 (ptpt) REVERT: E 331 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8903 (mtpp) REVERT: E 340 LYS cc_start: 0.8818 (mtpm) cc_final: 0.8268 (mttm) outliers start: 8 outliers final: 3 residues processed: 116 average time/residue: 1.7173 time to fit residues: 202.3477 Evaluate side-chains 118 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN C 362 HIS E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2915 Z= 0.119 Angle : 0.558 8.022 3900 Z= 0.258 Chirality : 0.048 0.124 440 Planarity : 0.002 0.017 495 Dihedral : 4.483 15.781 385 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 20.30 % 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: -1.29 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.001 PHE C 378 TYR 0.006 0.001 TYR B 310 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8640 (pttt) cc_final: 0.8343 (ptpt) REVERT: A 331 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8882 (mtpp) REVERT: B 317 LYS cc_start: 0.8779 (pttt) cc_final: 0.8525 (ptpp) REVERT: B 331 LYS cc_start: 0.9235 (mtmt) cc_final: 0.9000 (mtpp) REVERT: B 379 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7424 (mtt90) REVERT: C 317 LYS cc_start: 0.8799 (pttt) cc_final: 0.8559 (ptpp) REVERT: C 331 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8936 (mtpp) REVERT: C 379 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7243 (mtt90) REVERT: D 317 LYS cc_start: 0.8703 (pttt) cc_final: 0.8411 (ptpt) REVERT: D 331 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8860 (mtpp) REVERT: E 311 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8527 (mttt) REVERT: E 317 LYS cc_start: 0.8731 (pttt) cc_final: 0.8408 (ptpt) REVERT: E 331 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8902 (mtpp) REVERT: E 340 LYS cc_start: 0.8811 (mtpm) cc_final: 0.8260 (mttm) outliers start: 8 outliers final: 2 residues processed: 121 average time/residue: 1.6836 time to fit residues: 206.8998 Evaluate side-chains 115 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2915 Z= 0.142 Angle : 0.562 6.758 3900 Z= 0.262 Chirality : 0.048 0.124 440 Planarity : 0.002 0.012 495 Dihedral : 4.431 15.684 385 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 21.21 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 374 PHE 0.003 0.001 PHE C 378 TYR 0.007 0.001 TYR A 310 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8889 (mtpp) REVERT: B 317 LYS cc_start: 0.8726 (pttt) cc_final: 0.8473 (ptpp) REVERT: B 331 LYS cc_start: 0.9239 (mtmt) cc_final: 0.9000 (mtpp) REVERT: B 379 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7411 (mtt90) REVERT: C 317 LYS cc_start: 0.8799 (pttt) cc_final: 0.8564 (ptpp) REVERT: C 331 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8945 (mtpp) REVERT: C 379 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7196 (mtt90) REVERT: D 311 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8583 (ptpt) REVERT: D 317 LYS cc_start: 0.8718 (pttt) cc_final: 0.8431 (ptpt) REVERT: D 331 LYS cc_start: 0.9098 (mtmt) cc_final: 0.8868 (mtpp) REVERT: E 311 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8544 (mttt) REVERT: E 317 LYS cc_start: 0.8732 (pttt) cc_final: 0.8411 (ptpt) REVERT: E 331 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8903 (mtpp) REVERT: E 340 LYS cc_start: 0.8816 (mtpm) cc_final: 0.8270 (mttm) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 1.7574 time to fit residues: 206.9423 Evaluate side-chains 116 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2915 Z= 0.364 Angle : 0.688 7.473 3900 Z= 0.335 Chirality : 0.051 0.139 440 Planarity : 0.002 0.015 495 Dihedral : 4.954 17.090 385 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.52 % Allowed : 21.21 % 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: -1.29 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.007 0.001 PHE C 378 TYR 0.010 0.002 TYR B 310 ARG 0.004 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8886 (mtpp) REVERT: A 340 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8109 (mttm) REVERT: B 317 LYS cc_start: 0.8801 (pttt) cc_final: 0.8541 (ptpp) REVERT: B 331 LYS cc_start: 0.9245 (mtmt) cc_final: 0.9010 (mtpp) REVERT: B 379 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7522 (mtt90) REVERT: C 317 LYS cc_start: 0.8802 (pttt) cc_final: 0.8588 (ptpp) REVERT: C 331 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8955 (mtpp) REVERT: C 379 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7290 (mtt90) REVERT: D 317 LYS cc_start: 0.8793 (pttt) cc_final: 0.8472 (ptpt) REVERT: D 331 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8874 (mtpp) REVERT: E 311 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8555 (mttt) REVERT: E 317 LYS cc_start: 0.8798 (pttt) cc_final: 0.8432 (ptpt) REVERT: E 331 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8907 (mtpp) REVERT: E 340 LYS cc_start: 0.8822 (mtpm) cc_final: 0.8274 (mttm) outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 1.7064 time to fit residues: 202.6170 Evaluate side-chains 116 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2915 Z= 0.374 Angle : 0.698 7.364 3900 Z= 0.340 Chirality : 0.052 0.140 440 Planarity : 0.003 0.015 495 Dihedral : 5.023 16.792 385 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.61 % Allowed : 22.12 % 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: -1.29 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.007 0.001 PHE C 378 TYR 0.009 0.002 TYR B 310 ARG 0.004 0.001 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8884 (mtpp) REVERT: B 317 LYS cc_start: 0.8817 (pttt) cc_final: 0.8560 (ptpp) REVERT: B 331 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8987 (mtpp) REVERT: B 340 LYS cc_start: 0.8897 (mtpm) cc_final: 0.8268 (mttm) REVERT: B 379 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7537 (mtt90) REVERT: C 317 LYS cc_start: 0.8825 (pttt) cc_final: 0.8609 (ptpp) REVERT: C 331 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8981 (mtpp) REVERT: C 379 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7349 (mtt90) REVERT: D 317 LYS cc_start: 0.8793 (pttt) cc_final: 0.8455 (ptpt) REVERT: D 331 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8877 (mtpp) REVERT: E 311 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8555 (mttt) REVERT: E 317 LYS cc_start: 0.8807 (pttt) cc_final: 0.8441 (ptpt) REVERT: E 331 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8904 (mtpp) REVERT: E 340 LYS cc_start: 0.8816 (mtpm) cc_final: 0.8266 (mttm) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 1.8282 time to fit residues: 209.7430 Evaluate side-chains 116 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100827 restraints weight = 2980.763| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.54 r_work: 0.3334 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2915 Z= 0.137 Angle : 0.589 7.981 3900 Z= 0.274 Chirality : 0.049 0.122 440 Planarity : 0.002 0.013 495 Dihedral : 4.581 16.105 385 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.91 % Allowed : 23.03 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 374 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.001 TYR B 310 ARG 0.003 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.22 seconds wall clock time: 55 minutes 34.28 seconds (3334.28 seconds total)