Starting phenix.real_space_refine on Fri Aug 22 18:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_18263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_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/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_18263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_18263.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_18263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8w_18263/08_2025/8q8w_18263.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.62, per 1000 atoms: 0.24 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: 0.54 Conformation dependent library (CDL) restraints added in 254.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.23 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: 1.33 Time building geometry restraints manager: 0.73 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: 3.660 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: 0.030 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.080 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- 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= 0.666 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG E 349 TYR 0.061 0.013 TYR E 310 PHE 0.051 0.020 PHE F 346 HIS 0.013 0.003 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01063 ( 3297) covalent geometry : angle 1.75421 ( 4410) hydrogen bonds : bond 0.05338 ( 77) hydrogen bonds : angle 7.16877 ( 231) *********************** 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 to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.201 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: 1.6718 time to fit residues: 204.3752 Evaluate side-chains 84 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106661 restraints weight = 14077.051| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.59 r_work: 0.3554 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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= 0.171 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.001 ARG D 349 TYR 0.009 0.001 TYR B 310 PHE 0.007 0.001 PHE D 346 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3297) covalent geometry : angle 0.59262 ( 4410) hydrogen bonds : bond 0.02300 ( 77) hydrogen bonds : angle 4.85088 ( 231) *********************** 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 to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8350 (mttt) cc_final: 0.7869 (mtpp) REVERT: C 347 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8563 (mtmm) REVERT: A 317 LYS cc_start: 0.8363 (mttt) cc_final: 0.7981 (mtpp) REVERT: A 340 LYS cc_start: 0.8282 (mttt) cc_final: 0.7986 (mtpp) REVERT: D 317 LYS cc_start: 0.8400 (mttt) cc_final: 0.8189 (mttm) REVERT: D 375 LYS cc_start: 0.8756 (tttt) cc_final: 0.8526 (tttt) REVERT: E 317 LYS cc_start: 0.8230 (mttt) cc_final: 0.7623 (mtpp) REVERT: E 340 LYS cc_start: 0.8180 (mttt) cc_final: 0.7867 (mtpp) REVERT: E 345 ASP cc_start: 0.8385 (m-30) cc_final: 0.8101 (t0) REVERT: F 311 LYS cc_start: 0.8675 (mttt) cc_final: 0.7905 (mttm) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 1.8173 time to fit residues: 149.8675 Evaluate side-chains 61 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 9 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 A 327 ASN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109632 restraints weight = 11902.088| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.49 r_work: 0.3529 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3297 Z= 0.124 Angle : 0.534 6.150 4410 Z= 0.269 Chirality : 0.052 0.136 495 Planarity : 0.003 0.020 561 Dihedral : 5.457 15.200 435 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.88 % Allowed : 12.37 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 349 TYR 0.009 0.001 TYR B 310 PHE 0.009 0.002 PHE D 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3297) covalent geometry : angle 0.53376 ( 4410) hydrogen bonds : bond 0.01845 ( 77) hydrogen bonds : angle 4.47645 ( 231) *********************** 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 73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 347 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: A 317 LYS cc_start: 0.8457 (mttt) cc_final: 0.8085 (mtpp) REVERT: A 340 LYS cc_start: 0.8311 (mttt) cc_final: 0.8034 (mtpp) REVERT: A 345 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8041 (t0) REVERT: E 317 LYS cc_start: 0.8287 (mttt) cc_final: 0.7711 (mtpp) REVERT: E 340 LYS cc_start: 0.8096 (mttt) cc_final: 0.7811 (mtpt) REVERT: E 345 ASP cc_start: 0.8421 (m-30) cc_final: 0.8128 (t0) REVERT: F 311 LYS cc_start: 0.8630 (mttt) cc_final: 0.7867 (mttm) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.4943 time to fit residues: 105.3797 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.0670 overall best weight: 1.7324 ------------------------------------------------------------------------------- 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 F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109061 restraints weight = 11914.636| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.45 r_work: 0.3530 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3297 Z= 0.131 Angle : 0.505 6.118 4410 Z= 0.255 Chirality : 0.051 0.141 495 Planarity : 0.003 0.018 561 Dihedral : 5.152 15.802 435 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.42 % Allowed : 12.90 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.009 0.002 TYR B 310 PHE 0.006 0.001 PHE D 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3297) covalent geometry : angle 0.50511 ( 4410) hydrogen bonds : bond 0.01620 ( 77) hydrogen bonds : angle 4.20767 ( 231) *********************** 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 69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.198 Fit side-chains REVERT: C 347 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: A 317 LYS cc_start: 0.8479 (mttt) cc_final: 0.8093 (mtpp) REVERT: A 340 LYS cc_start: 0.8295 (mttt) cc_final: 0.8025 (mtpp) REVERT: A 345 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8057 (t0) REVERT: E 317 LYS cc_start: 0.8297 (mttt) cc_final: 0.7743 (mtpp) REVERT: E 340 LYS cc_start: 0.8094 (mttt) cc_final: 0.7811 (mtpt) REVERT: E 345 ASP cc_start: 0.8429 (m-30) cc_final: 0.8188 (t0) REVERT: F 311 LYS cc_start: 0.8641 (mttt) cc_final: 0.7870 (mttm) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 1.5437 time to fit residues: 102.5048 Evaluate side-chains 60 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 336 GLN F 307 GLN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110610 restraints weight = 11963.255| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.46 r_work: 0.3551 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4072 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= 0.092 Angle : 0.485 5.741 4410 Z= 0.241 Chirality : 0.052 0.137 495 Planarity : 0.003 0.019 561 Dihedral : 4.862 15.908 435 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.69 % Allowed : 13.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (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 ARG 0.001 0.000 ARG D 349 TYR 0.007 0.001 TYR B 310 PHE 0.004 0.001 PHE F 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3297) covalent geometry : angle 0.48481 ( 4410) hydrogen bonds : bond 0.01408 ( 77) hydrogen bonds : angle 4.09116 ( 231) *********************** 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 68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.208 Fit side-chains REVERT: C 347 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8575 (mtmm) REVERT: A 317 LYS cc_start: 0.8443 (mttt) cc_final: 0.8094 (mtpm) REVERT: A 340 LYS cc_start: 0.8286 (mttt) cc_final: 0.8008 (mtpp) REVERT: A 342 GLU cc_start: 0.8014 (tt0) cc_final: 0.7712 (tt0) REVERT: A 343 LYS cc_start: 0.8984 (mttp) cc_final: 0.8707 (mtpt) REVERT: A 345 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8076 (t0) REVERT: D 348 ASP cc_start: 0.8467 (t0) cc_final: 0.8254 (t0) REVERT: E 317 LYS cc_start: 0.8279 (mttt) cc_final: 0.7697 (mtpp) REVERT: E 340 LYS cc_start: 0.8092 (mttt) cc_final: 0.7794 (mtpt) REVERT: E 345 ASP cc_start: 0.8400 (m-30) cc_final: 0.8143 (t0) REVERT: F 311 LYS cc_start: 0.8580 (mttt) cc_final: 0.7819 (mttm) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 1.6674 time to fit residues: 107.1762 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS 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 F residue 315 LEU 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 14 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 A 327 ASN D 336 GLN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110655 restraints weight = 11952.233| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.45 r_work: 0.3547 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.4195 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= 0.096 Angle : 0.474 5.656 4410 Z= 0.236 Chirality : 0.051 0.132 495 Planarity : 0.003 0.026 561 Dihedral : 4.639 15.168 435 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.88 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.007 0.001 TYR B 310 PHE 0.005 0.001 PHE F 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3297) covalent geometry : angle 0.47382 ( 4410) hydrogen bonds : bond 0.01280 ( 77) hydrogen bonds : angle 3.91906 ( 231) *********************** 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 68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.197 Fit side-chains REVERT: C 347 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8495 (mttm) REVERT: A 317 LYS cc_start: 0.8448 (mttt) cc_final: 0.8110 (mtpm) REVERT: A 340 LYS cc_start: 0.8310 (mttt) cc_final: 0.8009 (mtpp) REVERT: A 342 GLU cc_start: 0.8040 (tt0) cc_final: 0.7740 (tt0) REVERT: A 345 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8053 (t70) REVERT: D 348 ASP cc_start: 0.8477 (t0) cc_final: 0.8250 (t0) REVERT: E 317 LYS cc_start: 0.8293 (mttt) cc_final: 0.7733 (mtpp) REVERT: E 340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7836 (mtpt) REVERT: E 345 ASP cc_start: 0.8375 (m-30) cc_final: 0.8159 (t0) REVERT: F 311 LYS cc_start: 0.8587 (mttt) cc_final: 0.7832 (mttm) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 1.6347 time to fit residues: 108.4354 Evaluate side-chains 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 336 GLN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.112191 restraints weight = 11792.133| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.44 r_work: 0.3573 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3297 Z= 0.074 Angle : 0.449 4.945 4410 Z= 0.223 Chirality : 0.052 0.132 495 Planarity : 0.003 0.034 561 Dihedral : 4.384 13.343 435 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.88 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.000 0.000 ARG D 349 TYR 0.006 0.001 TYR B 310 PHE 0.003 0.000 PHE E 346 HIS 0.004 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 3297) covalent geometry : angle 0.44949 ( 4410) hydrogen bonds : bond 0.01136 ( 77) hydrogen bonds : angle 3.70552 ( 231) *********************** 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 71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.212 Fit side-chains REVERT: C 347 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8485 (mttm) REVERT: A 317 LYS cc_start: 0.8366 (mttt) cc_final: 0.8027 (mtpm) REVERT: A 340 LYS cc_start: 0.8318 (mttt) cc_final: 0.8023 (mtpp) REVERT: A 342 GLU cc_start: 0.8014 (tt0) cc_final: 0.7643 (tt0) REVERT: A 345 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8044 (t70) REVERT: D 348 ASP cc_start: 0.8478 (t0) cc_final: 0.8217 (t0) REVERT: E 317 LYS cc_start: 0.8251 (mttt) cc_final: 0.7718 (mtpp) REVERT: E 340 LYS cc_start: 0.8076 (mttt) cc_final: 0.7775 (mtpt) REVERT: E 345 ASP cc_start: 0.8369 (m-30) cc_final: 0.8151 (t0) REVERT: F 311 LYS cc_start: 0.8558 (mttt) cc_final: 0.7792 (mttm) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 1.5709 time to fit residues: 107.4685 Evaluate side-chains 68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 315 LEU 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 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 F 307 GLN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.118251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109127 restraints weight = 12079.082| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.46 r_work: 0.3525 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3297 Z= 0.134 Angle : 0.472 4.715 4410 Z= 0.236 Chirality : 0.050 0.128 495 Planarity : 0.003 0.036 561 Dihedral : 4.441 12.998 435 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.61 % Allowed : 16.13 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.009 0.002 TYR B 310 PHE 0.008 0.001 PHE F 346 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3297) covalent geometry : angle 0.47154 ( 4410) hydrogen bonds : bond 0.01291 ( 77) hydrogen bonds : angle 3.60748 ( 231) *********************** 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 66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.208 Fit side-chains REVERT: A 311 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (pttt) REVERT: A 317 LYS cc_start: 0.8450 (mttt) cc_final: 0.8123 (mtpm) REVERT: A 340 LYS cc_start: 0.8324 (mttt) cc_final: 0.8014 (mtpp) REVERT: A 345 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8033 (t0) REVERT: E 317 LYS cc_start: 0.8261 (mttt) cc_final: 0.7754 (mtpp) REVERT: E 340 LYS cc_start: 0.8116 (mttt) cc_final: 0.7819 (mtpt) REVERT: E 345 ASP cc_start: 0.8366 (m-30) cc_final: 0.8161 (t0) REVERT: F 311 LYS cc_start: 0.8625 (mttt) cc_final: 0.7866 (mttm) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 1.6731 time to fit residues: 105.8182 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 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 F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109097 restraints weight = 11998.415| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.46 r_work: 0.3526 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4488 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= 0.107 Angle : 0.462 4.523 4410 Z= 0.230 Chirality : 0.051 0.128 495 Planarity : 0.003 0.036 561 Dihedral : 4.379 12.748 435 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.08 % Allowed : 16.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.007 0.001 TYR B 310 PHE 0.005 0.001 PHE F 346 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3297) covalent geometry : angle 0.46249 ( 4410) hydrogen bonds : bond 0.01217 ( 77) hydrogen bonds : angle 3.44810 ( 231) *********************** 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 66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.195 Fit side-chains REVERT: A 317 LYS cc_start: 0.8444 (mttt) cc_final: 0.8108 (mtpm) REVERT: A 340 LYS cc_start: 0.8361 (mttt) cc_final: 0.8042 (mtpp) REVERT: A 345 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8046 (t0) REVERT: D 348 ASP cc_start: 0.8497 (t0) cc_final: 0.8279 (t0) REVERT: E 317 LYS cc_start: 0.8276 (mttt) cc_final: 0.7790 (mtpp) REVERT: E 340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7829 (mtpt) REVERT: E 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.8158 (t0) REVERT: F 311 LYS cc_start: 0.8630 (mttt) cc_final: 0.7867 (mttm) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 1.5949 time to fit residues: 104.2416 Evaluate side-chains 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 5 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 F 307 GLN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108887 restraints weight = 12064.763| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.46 r_work: 0.3527 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3297 Z= 0.115 Angle : 0.463 5.057 4410 Z= 0.231 Chirality : 0.050 0.127 495 Planarity : 0.003 0.043 561 Dihedral : 4.348 12.735 435 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.61 % Allowed : 16.40 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.007 0.002 TYR B 310 PHE 0.006 0.001 PHE F 346 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3297) covalent geometry : angle 0.46279 ( 4410) hydrogen bonds : bond 0.01260 ( 77) hydrogen bonds : angle 3.40630 ( 231) ********************** 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 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.178 Fit side-chains REVERT: A 317 LYS cc_start: 0.8429 (mttt) cc_final: 0.8094 (mtpm) REVERT: A 340 LYS cc_start: 0.8370 (mttt) cc_final: 0.8043 (mtpp) REVERT: A 345 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8039 (t0) REVERT: D 348 ASP cc_start: 0.8499 (t0) cc_final: 0.8274 (t0) REVERT: E 317 LYS cc_start: 0.8248 (mttt) cc_final: 0.7778 (mtpp) REVERT: E 340 LYS cc_start: 0.8110 (mttt) cc_final: 0.7810 (mtpt) REVERT: E 345 ASP cc_start: 0.8373 (m-30) cc_final: 0.8154 (t0) REVERT: F 311 LYS cc_start: 0.8653 (mttt) cc_final: 0.7877 (mttm) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 1.6059 time to fit residues: 99.9260 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110325 restraints weight = 11931.407| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.45 r_work: 0.3550 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3297 Z= 0.082 Angle : 0.449 4.835 4410 Z= 0.223 Chirality : 0.051 0.129 495 Planarity : 0.003 0.048 561 Dihedral : 4.191 12.518 435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.61 % Allowed : 16.40 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.000 0.000 ARG E 349 TYR 0.005 0.001 TYR B 310 PHE 0.003 0.001 PHE F 346 HIS 0.001 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 3297) covalent geometry : angle 0.44876 ( 4410) hydrogen bonds : bond 0.01130 ( 77) hydrogen bonds : angle 3.37724 ( 231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.10 seconds wall clock time: 62 minutes 11.48 seconds (3731.48 seconds total)