Starting phenix.real_space_refine on Tue Sep 24 02:53:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/09_2024/8q8w_18263.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2034 2.51 5 N 594 2.21 5 O 612 1.98 5 H 3372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 5.09, per 1000 atoms: 0.77 Number of scatterers: 6618 At special positions: 0 Unit cell: (121.952, 140.904, 45.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 612 8.00 N 594 7.00 C 2034 6.00 H 3372 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.70 Conformation dependent library (CDL) restraints added in 632.9 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.620A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.702A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.363A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS C 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.546A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.518A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL E 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.397A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.592A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.771A pdb=" N ASP A 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 374 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.522A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.305A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.606A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 removed outlier: 6.777A pdb=" N GLY B 333 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.592A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.290A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.273A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.376A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 231 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: 2.74 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3366 1.12 - 1.29: 546 1.29 - 1.47: 1076 1.47 - 1.64: 1675 1.64 - 1.81: 6 Bond restraints: 6669 Sorted by residual: bond pdb=" NE2 GLN E 336 " pdb="HE22 GLN E 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 326 " pdb=" H GLY B 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY C 333 " pdb=" H GLY C 333 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 327 " pdb="HD21 ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY A 355 " pdb=" H GLY A 355 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 10465 2.61 - 5.21: 1316 5.21 - 7.82: 374 7.82 - 10.43: 7 10.43 - 13.04: 6 Bond angle restraints: 12168 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" OE1 GLN F 336 " pdb=" CD GLN F 336 " pdb=" NE2 GLN F 336 " ideal model delta sigma weight residual 122.60 117.91 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" OE1 GLN D 336 " pdb=" CD GLN D 336 " pdb=" NE2 GLN D 336 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 2696 13.72 - 27.45: 179 27.45 - 41.17: 69 41.17 - 54.89: 56 54.89 - 68.61: 72 Dihedral angle restraints: 3072 sinusoidal: 1758 harmonic: 1314 Sorted by residual: dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU D 372 " pdb=" C GLU D 372 " pdb=" N THR D 373 " pdb=" CA THR D 373 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU F 372 " pdb=" C GLU F 372 " pdb=" N THR F 373 " pdb=" CA THR F 373 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 220 0.053 - 0.106: 180 0.106 - 0.160: 61 0.160 - 0.213: 26 0.213 - 0.266: 8 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA SER B 352 " pdb=" N SER B 352 " pdb=" C SER B 352 " pdb=" CB SER B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 492 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.052 2.00e-02 2.50e+03 4.88e-02 3.58e+01 pdb=" CG ASN A 368 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.048 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.035 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " -0.061 2.00e-02 2.50e+03 3.69e-02 3.06e+01 pdb=" CG HIS D 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 362 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS D 362 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 HIS D 362 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.066 2.00e-02 2.50e+03 2.96e-02 2.62e+01 pdb=" CG TYR E 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.058 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.002 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 395 2.14 - 2.76: 10601 2.76 - 3.37: 17256 3.37 - 3.99: 23349 3.99 - 4.60: 32273 Nonbonded interactions: 83874 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.526 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.553 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.614 2.450 ... (remaining 83869 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' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) } 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: 20.270 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 0.035 3297 Z= 0.715 Angle : 1.754 6.483 4410 Z= 1.171 Chirality : 0.085 0.266 495 Planarity : 0.009 0.034 561 Dihedral : 11.104 67.181 1263 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.38 (0.35), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 330 PHE 0.051 0.020 PHE F 346 TYR 0.061 0.013 TYR E 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8013 (mttt) cc_final: 0.7209 (mtpp) REVERT: C 340 LYS cc_start: 0.8388 (mttt) cc_final: 0.7772 (mtpp) REVERT: C 343 LYS cc_start: 0.8441 (mttt) cc_final: 0.8221 (mttp) REVERT: C 370 LYS cc_start: 0.7613 (tttt) cc_final: 0.7329 (ttpt) REVERT: B 321 LYS cc_start: 0.7034 (mttt) cc_final: 0.6649 (mttt) REVERT: B 336 GLN cc_start: 0.7457 (tt0) cc_final: 0.7246 (tt0) REVERT: B 340 LYS cc_start: 0.6971 (mttt) cc_final: 0.6574 (mtpp) REVERT: A 317 LYS cc_start: 0.7134 (mttt) cc_final: 0.6503 (mtpp) REVERT: A 340 LYS cc_start: 0.7295 (mttt) cc_final: 0.6722 (mtpp) REVERT: A 375 LYS cc_start: 0.7016 (tttt) cc_final: 0.6776 (ttpp) REVERT: D 314 ASP cc_start: 0.7989 (t0) cc_final: 0.7645 (t0) REVERT: D 317 LYS cc_start: 0.8030 (mttt) cc_final: 0.7675 (mttm) REVERT: D 336 GLN cc_start: 0.7876 (tt0) cc_final: 0.7591 (tt0) REVERT: D 338 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 340 LYS cc_start: 0.7769 (mttt) cc_final: 0.7447 (mtpp) REVERT: D 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.8103 (tttt) REVERT: E 317 LYS cc_start: 0.6968 (mttt) cc_final: 0.6166 (mtpp) REVERT: E 340 LYS cc_start: 0.7166 (mttt) cc_final: 0.6568 (mtpp) REVERT: E 347 LYS cc_start: 0.8436 (mttt) cc_final: 0.8188 (mttm) REVERT: F 311 LYS cc_start: 0.8233 (mttt) cc_final: 0.7177 (mttm) REVERT: F 317 LYS cc_start: 0.6777 (mttt) cc_final: 0.6569 (mtmt) REVERT: F 336 GLN cc_start: 0.7466 (tt0) cc_final: 0.6999 (tt0) REVERT: F 340 LYS cc_start: 0.7054 (mttt) cc_final: 0.6796 (mtpp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 3.1833 time to fit residues: 390.0106 Evaluate side-chains 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 327 ASN D 307 GLN D 327 ASN F 307 GLN F 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3297 Z= 0.269 Angle : 0.593 6.156 4410 Z= 0.306 Chirality : 0.051 0.136 495 Planarity : 0.004 0.026 561 Dihedral : 6.178 16.422 435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.08 % Allowed : 10.22 % Favored : 88.71 % 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: -1.00 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE D 346 TYR 0.009 0.001 TYR B 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.7967 (mttt) cc_final: 0.7159 (mtpp) REVERT: C 340 LYS cc_start: 0.8343 (mttt) cc_final: 0.7748 (mtpp) REVERT: C 343 LYS cc_start: 0.8349 (mttt) cc_final: 0.8148 (mttp) REVERT: C 347 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: B 314 ASP cc_start: 0.7892 (t0) cc_final: 0.7682 (t0) REVERT: B 336 GLN cc_start: 0.7435 (tt0) cc_final: 0.7214 (tt0) REVERT: B 340 LYS cc_start: 0.7010 (mttt) cc_final: 0.6644 (mtpp) REVERT: B 342 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7076 (tt0) REVERT: A 317 LYS cc_start: 0.7359 (mttt) cc_final: 0.6748 (mtpp) REVERT: A 340 LYS cc_start: 0.7515 (mttt) cc_final: 0.6919 (mtpp) REVERT: A 375 LYS cc_start: 0.6991 (tttt) cc_final: 0.6779 (ttpp) REVERT: D 317 LYS cc_start: 0.7979 (mttt) cc_final: 0.7634 (mttm) REVERT: D 340 LYS cc_start: 0.7776 (mttt) cc_final: 0.7451 (mtpp) REVERT: D 353 LYS cc_start: 0.7573 (mttt) cc_final: 0.6920 (tttp) REVERT: D 375 LYS cc_start: 0.8402 (tttt) cc_final: 0.8076 (tttt) REVERT: E 317 LYS cc_start: 0.7168 (mttt) cc_final: 0.6352 (mtpp) REVERT: E 340 LYS cc_start: 0.7246 (mttt) cc_final: 0.6640 (mtpp) REVERT: E 345 ASP cc_start: 0.7824 (m-30) cc_final: 0.7441 (t0) REVERT: E 347 LYS cc_start: 0.8363 (mttt) cc_final: 0.8124 (mttm) REVERT: F 311 LYS cc_start: 0.8255 (mttt) cc_final: 0.7148 (mttm) REVERT: F 336 GLN cc_start: 0.7494 (tt0) cc_final: 0.6995 (tt0) REVERT: F 340 LYS cc_start: 0.7081 (mttt) cc_final: 0.6784 (mtpp) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 3.4427 time to fit residues: 284.5583 Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN B 307 GLN A 327 ASN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3297 Z= 0.255 Angle : 0.531 6.021 4410 Z= 0.274 Chirality : 0.052 0.129 495 Planarity : 0.003 0.020 561 Dihedral : 5.371 15.436 435 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.88 % Allowed : 10.48 % Favored : 87.63 % 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: -0.98 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.013 0.002 PHE D 346 TYR 0.011 0.002 TYR B 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8282 (t0) cc_final: 0.8020 (t0) REVERT: C 317 LYS cc_start: 0.7909 (mttt) cc_final: 0.7115 (mtpp) REVERT: C 340 LYS cc_start: 0.8396 (mttt) cc_final: 0.7798 (mtpp) REVERT: C 343 LYS cc_start: 0.8362 (mttt) cc_final: 0.8149 (mttp) REVERT: C 347 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: C 370 LYS cc_start: 0.7588 (tttt) cc_final: 0.7198 (ttpt) REVERT: B 336 GLN cc_start: 0.7439 (tt0) cc_final: 0.7196 (tt0) REVERT: B 340 LYS cc_start: 0.6933 (mttt) cc_final: 0.6581 (mtpp) REVERT: B 353 LYS cc_start: 0.6976 (mttt) cc_final: 0.6191 (tttp) REVERT: A 317 LYS cc_start: 0.7634 (mttt) cc_final: 0.6989 (mtpp) REVERT: A 340 LYS cc_start: 0.7590 (mttt) cc_final: 0.6962 (mtpp) REVERT: A 345 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7427 (t70) REVERT: D 317 LYS cc_start: 0.7942 (mttt) cc_final: 0.7581 (mttp) REVERT: D 340 LYS cc_start: 0.7760 (mttt) cc_final: 0.7425 (mtpp) REVERT: D 375 LYS cc_start: 0.8455 (tttt) cc_final: 0.8130 (tttt) REVERT: E 317 LYS cc_start: 0.7320 (mttt) cc_final: 0.6489 (mtpp) REVERT: E 340 LYS cc_start: 0.7232 (mttt) cc_final: 0.6644 (mtpp) REVERT: E 345 ASP cc_start: 0.7858 (m-30) cc_final: 0.7483 (t0) REVERT: F 311 LYS cc_start: 0.8261 (mttt) cc_final: 0.7150 (mttm) REVERT: F 336 GLN cc_start: 0.7491 (tt0) cc_final: 0.7039 (tt0) REVERT: F 340 LYS cc_start: 0.7061 (mttt) cc_final: 0.6775 (mtpp) REVERT: F 353 LYS cc_start: 0.7280 (mttt) cc_final: 0.6461 (tttp) outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 3.2666 time to fit residues: 266.7308 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3297 Z= 0.200 Angle : 0.488 6.190 4410 Z= 0.247 Chirality : 0.051 0.128 495 Planarity : 0.003 0.019 561 Dihedral : 5.101 15.195 435 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.15 % Allowed : 11.56 % Favored : 86.29 % 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: -0.88 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 374 PHE 0.006 0.001 PHE D 346 TYR 0.008 0.002 TYR B 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8297 (t0) cc_final: 0.8096 (t0) REVERT: C 317 LYS cc_start: 0.7905 (mttt) cc_final: 0.7105 (mtpp) REVERT: C 340 LYS cc_start: 0.8409 (mttt) cc_final: 0.7799 (mtpp) REVERT: C 343 LYS cc_start: 0.8361 (mttt) cc_final: 0.8147 (mttp) REVERT: C 347 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8331 (mtmm) REVERT: B 340 LYS cc_start: 0.6919 (mttt) cc_final: 0.6568 (mtpp) REVERT: A 317 LYS cc_start: 0.7625 (mttt) cc_final: 0.6992 (mtpp) REVERT: A 340 LYS cc_start: 0.7586 (mttt) cc_final: 0.6950 (mtpp) REVERT: A 342 GLU cc_start: 0.7384 (tt0) cc_final: 0.6867 (tt0) REVERT: A 345 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7433 (t70) REVERT: D 317 LYS cc_start: 0.7895 (mttt) cc_final: 0.7527 (mttm) REVERT: D 340 LYS cc_start: 0.7770 (mttt) cc_final: 0.7432 (mtpp) REVERT: D 353 LYS cc_start: 0.7572 (mttt) cc_final: 0.6918 (tttp) REVERT: D 375 LYS cc_start: 0.8469 (tttt) cc_final: 0.8142 (tttt) REVERT: E 317 LYS cc_start: 0.7358 (mttt) cc_final: 0.6537 (mtpp) REVERT: E 340 LYS cc_start: 0.7202 (mttt) cc_final: 0.6555 (mtpt) REVERT: E 345 ASP cc_start: 0.7879 (m-30) cc_final: 0.7435 (t0) REVERT: F 311 LYS cc_start: 0.8236 (mttt) cc_final: 0.7137 (mttm) REVERT: F 336 GLN cc_start: 0.7462 (tt0) cc_final: 0.6966 (tt0) REVERT: F 340 LYS cc_start: 0.7045 (mttt) cc_final: 0.6744 (mtpp) outliers start: 8 outliers final: 1 residues processed: 75 average time/residue: 3.2624 time to fit residues: 249.7128 Evaluate side-chains 69 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN A 327 ASN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.142 Angle : 0.454 6.094 4410 Z= 0.230 Chirality : 0.052 0.128 495 Planarity : 0.002 0.018 561 Dihedral : 4.717 14.232 435 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.34 % Allowed : 12.37 % Favored : 86.29 % 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: -0.80 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.005 0.001 PHE F 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8293 (t0) cc_final: 0.8059 (t0) REVERT: C 317 LYS cc_start: 0.7772 (mttt) cc_final: 0.7011 (mtpp) REVERT: C 340 LYS cc_start: 0.8404 (mttt) cc_final: 0.7725 (mtpt) REVERT: C 343 LYS cc_start: 0.8368 (mttt) cc_final: 0.8154 (mttp) REVERT: C 347 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8341 (mtmm) REVERT: B 340 LYS cc_start: 0.6869 (mttt) cc_final: 0.6519 (mtpp) REVERT: A 317 LYS cc_start: 0.7615 (mttt) cc_final: 0.6988 (mtpp) REVERT: A 340 LYS cc_start: 0.7607 (mttt) cc_final: 0.6979 (mtpp) REVERT: A 345 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7472 (t0) REVERT: D 317 LYS cc_start: 0.7794 (mttt) cc_final: 0.7427 (mttp) REVERT: D 340 LYS cc_start: 0.7765 (mttt) cc_final: 0.7421 (mtpp) REVERT: D 353 LYS cc_start: 0.7567 (mttt) cc_final: 0.6922 (tttp) REVERT: D 375 LYS cc_start: 0.8462 (tttt) cc_final: 0.8145 (tttt) REVERT: E 317 LYS cc_start: 0.7368 (mttt) cc_final: 0.6592 (mtpp) REVERT: E 340 LYS cc_start: 0.7207 (mttt) cc_final: 0.6553 (mtpt) REVERT: E 345 ASP cc_start: 0.7872 (m-30) cc_final: 0.7474 (t0) REVERT: F 311 LYS cc_start: 0.8200 (mttt) cc_final: 0.7098 (mttm) REVERT: F 336 GLN cc_start: 0.7449 (tt0) cc_final: 0.7058 (tt0) REVERT: F 340 LYS cc_start: 0.7066 (mttt) cc_final: 0.6757 (mtpp) outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 3.3203 time to fit residues: 254.1687 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3297 Z= 0.259 Angle : 0.484 5.859 4410 Z= 0.246 Chirality : 0.050 0.128 495 Planarity : 0.003 0.018 561 Dihedral : 4.796 14.722 435 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.88 % Allowed : 13.71 % Favored : 84.41 % 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: -0.82 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.008 0.001 PHE F 346 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: C 317 LYS cc_start: 0.7887 (mttt) cc_final: 0.7107 (mtpp) REVERT: C 340 LYS cc_start: 0.8395 (mttt) cc_final: 0.7803 (mtpp) REVERT: C 343 LYS cc_start: 0.8327 (mttt) cc_final: 0.8112 (mttp) REVERT: C 347 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8358 (mtmm) REVERT: B 340 LYS cc_start: 0.6847 (mttt) cc_final: 0.6512 (mtpp) REVERT: B 342 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7132 (tt0) REVERT: A 317 LYS cc_start: 0.7616 (mttt) cc_final: 0.7056 (mtpm) REVERT: A 340 LYS cc_start: 0.7559 (mttt) cc_final: 0.6918 (mtpp) REVERT: A 345 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7437 (t0) REVERT: D 317 LYS cc_start: 0.7910 (mttt) cc_final: 0.7519 (mttm) REVERT: D 340 LYS cc_start: 0.7822 (mttt) cc_final: 0.7432 (mtpp) REVERT: D 353 LYS cc_start: 0.7578 (mttt) cc_final: 0.6929 (tttp) REVERT: D 375 LYS cc_start: 0.8485 (tttt) cc_final: 0.8168 (tttt) REVERT: E 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.6622 (mtpp) REVERT: E 340 LYS cc_start: 0.7213 (mttt) cc_final: 0.6557 (mtpt) REVERT: E 345 ASP cc_start: 0.7858 (m-30) cc_final: 0.7461 (t0) REVERT: F 311 LYS cc_start: 0.8228 (mttt) cc_final: 0.7139 (mttm) REVERT: F 336 GLN cc_start: 0.7506 (tt0) cc_final: 0.7099 (tt0) REVERT: F 340 LYS cc_start: 0.7047 (mttt) cc_final: 0.6711 (mtpp) REVERT: F 353 LYS cc_start: 0.7238 (mttt) cc_final: 0.6553 (tttp) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 3.3402 time to fit residues: 245.4437 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN D 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3297 Z= 0.156 Angle : 0.457 5.875 4410 Z= 0.230 Chirality : 0.051 0.130 495 Planarity : 0.002 0.017 561 Dihedral : 4.586 14.367 435 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.61 % Allowed : 14.25 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.005 0.001 PHE F 346 TYR 0.007 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8334 (t0) cc_final: 0.8129 (t0) REVERT: C 317 LYS cc_start: 0.7783 (mttt) cc_final: 0.7045 (mtpp) REVERT: C 340 LYS cc_start: 0.8401 (mttt) cc_final: 0.7803 (mtpp) REVERT: B 340 LYS cc_start: 0.6836 (mttt) cc_final: 0.6514 (mtpp) REVERT: B 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7141 (tt0) REVERT: A 317 LYS cc_start: 0.7576 (mttt) cc_final: 0.7038 (mtpm) REVERT: A 340 LYS cc_start: 0.7618 (mttt) cc_final: 0.6950 (mtpp) REVERT: A 345 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7447 (t0) REVERT: D 317 LYS cc_start: 0.7879 (mttt) cc_final: 0.7496 (mttm) REVERT: D 340 LYS cc_start: 0.7800 (mttt) cc_final: 0.7424 (mtpp) REVERT: D 353 LYS cc_start: 0.7591 (mttt) cc_final: 0.6940 (tttp) REVERT: D 375 LYS cc_start: 0.8481 (tttt) cc_final: 0.8168 (tttt) REVERT: E 317 LYS cc_start: 0.7401 (mttt) cc_final: 0.6653 (mtpp) REVERT: E 340 LYS cc_start: 0.7209 (mttt) cc_final: 0.6557 (mtpt) REVERT: E 345 ASP cc_start: 0.7858 (m-30) cc_final: 0.7463 (t0) REVERT: F 311 LYS cc_start: 0.8220 (mttt) cc_final: 0.7117 (mttm) REVERT: F 336 GLN cc_start: 0.7484 (tt0) cc_final: 0.6999 (tt0) REVERT: F 340 LYS cc_start: 0.7042 (mttt) cc_final: 0.6706 (mtpp) REVERT: F 353 LYS cc_start: 0.7247 (mttt) cc_final: 0.6544 (tttm) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 3.4125 time to fit residues: 254.1271 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.106 Angle : 0.435 5.391 4410 Z= 0.216 Chirality : 0.052 0.129 495 Planarity : 0.002 0.024 561 Dihedral : 4.280 13.635 435 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.08 % Allowed : 14.78 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 374 PHE 0.001 0.000 PHE F 346 TYR 0.005 0.001 TYR A 310 ARG 0.003 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8326 (t0) cc_final: 0.8079 (t0) REVERT: C 317 LYS cc_start: 0.7677 (mttt) cc_final: 0.6948 (mtpp) REVERT: C 340 LYS cc_start: 0.8369 (mttt) cc_final: 0.7746 (mtpt) REVERT: B 340 LYS cc_start: 0.6781 (mttt) cc_final: 0.6469 (mtpp) REVERT: B 342 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7194 (tt0) REVERT: A 317 LYS cc_start: 0.7669 (mttt) cc_final: 0.7102 (mtpm) REVERT: A 340 LYS cc_start: 0.7715 (mttt) cc_final: 0.7048 (mtpp) REVERT: A 345 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7439 (t0) REVERT: D 317 LYS cc_start: 0.7770 (mttt) cc_final: 0.7390 (mttm) REVERT: D 340 LYS cc_start: 0.7789 (mttt) cc_final: 0.7422 (mtpp) REVERT: D 375 LYS cc_start: 0.8488 (tttt) cc_final: 0.8178 (tttt) REVERT: E 317 LYS cc_start: 0.7457 (mttt) cc_final: 0.6721 (mtpp) REVERT: E 340 LYS cc_start: 0.7185 (mttt) cc_final: 0.6546 (mtpt) REVERT: E 345 ASP cc_start: 0.7847 (m-30) cc_final: 0.7487 (t0) REVERT: F 311 LYS cc_start: 0.8190 (mttt) cc_final: 0.7090 (mttm) REVERT: F 336 GLN cc_start: 0.7447 (tt0) cc_final: 0.7019 (tt0) REVERT: F 340 LYS cc_start: 0.7029 (mttt) cc_final: 0.6702 (mtpp) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 3.3608 time to fit residues: 243.4561 Evaluate side-chains 72 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3297 Z= 0.130 Angle : 0.428 5.355 4410 Z= 0.215 Chirality : 0.051 0.125 495 Planarity : 0.003 0.032 561 Dihedral : 4.245 13.510 435 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.08 % Allowed : 15.59 % Favored : 83.33 % 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: -0.71 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.004 0.001 PHE F 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8250 (t0) cc_final: 0.8007 (t0) REVERT: C 317 LYS cc_start: 0.7682 (mttt) cc_final: 0.6971 (mtpp) REVERT: C 340 LYS cc_start: 0.8376 (mttt) cc_final: 0.7791 (mtpp) REVERT: B 340 LYS cc_start: 0.6784 (mttt) cc_final: 0.6474 (mtpp) REVERT: B 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7169 (tt0) REVERT: A 317 LYS cc_start: 0.7690 (mttt) cc_final: 0.7125 (mtpm) REVERT: A 340 LYS cc_start: 0.7703 (mttt) cc_final: 0.7046 (mtpp) REVERT: A 345 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7444 (t0) REVERT: D 340 LYS cc_start: 0.7783 (mttt) cc_final: 0.7409 (mtpp) REVERT: D 375 LYS cc_start: 0.8475 (tttt) cc_final: 0.8168 (tttt) REVERT: E 317 LYS cc_start: 0.7471 (mttt) cc_final: 0.6751 (mtpp) REVERT: E 340 LYS cc_start: 0.7179 (mttt) cc_final: 0.6528 (mtpt) REVERT: E 345 ASP cc_start: 0.7845 (m-30) cc_final: 0.7491 (t0) REVERT: F 311 LYS cc_start: 0.8180 (mttt) cc_final: 0.7091 (mttm) REVERT: F 336 GLN cc_start: 0.7472 (tt0) cc_final: 0.7050 (tt0) REVERT: F 340 LYS cc_start: 0.7027 (mttt) cc_final: 0.6699 (mtpp) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 3.2639 time to fit residues: 243.3032 Evaluate side-chains 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.0070 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3297 Z= 0.146 Angle : 0.435 5.085 4410 Z= 0.219 Chirality : 0.051 0.127 495 Planarity : 0.003 0.039 561 Dihedral : 4.240 13.785 435 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 15.32 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.39), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.005 0.001 PHE F 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.8270 (t0) cc_final: 0.8031 (t0) REVERT: C 317 LYS cc_start: 0.7762 (mttt) cc_final: 0.7054 (mtpp) REVERT: C 340 LYS cc_start: 0.8373 (mttt) cc_final: 0.7755 (mtpt) REVERT: B 340 LYS cc_start: 0.6812 (mttt) cc_final: 0.6508 (mtpp) REVERT: B 342 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7163 (tt0) REVERT: A 317 LYS cc_start: 0.7632 (mttt) cc_final: 0.7097 (mtpm) REVERT: A 340 LYS cc_start: 0.7637 (mttt) cc_final: 0.6990 (mtpp) REVERT: A 345 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7452 (t70) REVERT: D 340 LYS cc_start: 0.7800 (mttt) cc_final: 0.7426 (mtpp) REVERT: D 375 LYS cc_start: 0.8456 (tttt) cc_final: 0.8146 (tttt) REVERT: E 317 LYS cc_start: 0.7449 (mttt) cc_final: 0.6757 (mtpp) REVERT: E 340 LYS cc_start: 0.7175 (mttt) cc_final: 0.6544 (mtpt) REVERT: E 345 ASP cc_start: 0.7848 (m-30) cc_final: 0.7496 (t0) REVERT: F 311 LYS cc_start: 0.8188 (mttt) cc_final: 0.7092 (mttm) REVERT: F 336 GLN cc_start: 0.7487 (tt0) cc_final: 0.7062 (tt0) REVERT: F 340 LYS cc_start: 0.7064 (mttt) cc_final: 0.6734 (mtpp) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 3.3360 time to fit residues: 262.1280 Evaluate side-chains 75 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN D 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111928 restraints weight = 13112.688| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.49 r_work: 0.3631 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.110 Angle : 0.422 4.792 4410 Z= 0.211 Chirality : 0.051 0.128 495 Planarity : 0.003 0.042 561 Dihedral : 4.065 13.288 435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.08 % Allowed : 15.86 % Favored : 83.06 % 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: -0.67 (0.39), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 330 PHE 0.002 0.000 PHE D 346 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5265.87 seconds wall clock time: 94 minutes 24.16 seconds (5664.16 seconds total)