Starting phenix.real_space_refine on Tue Mar 11 21:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8w_18263/03_2025/8q8w_18263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8w_18263/03_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_18263/03_2025/8q8w_18263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8w_18263/03_2025/8q8w_18263.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8w_18263/03_2025/8q8w_18263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8w_18263/03_2025/8q8w_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-5624/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: 4.57, per 1000 atoms: 0.69 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: 1.77 Conformation dependent library (CDL) restraints added in 603.0 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: 0.60 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: 1.83 Time building geometry restraints manager: 2.04 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: 0.01 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.860 Find NCS groups from input model: 0.160 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.607 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: 3.2222 time to fit residues: 394.6223 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 : 0.556 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 3.9990 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: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107516 restraints weight = 13901.871| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.57 r_work: 0.3565 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2730 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= 0.225 Angle : 0.593 6.131 4410 Z= 0.307 Chirality : 0.051 0.134 495 Planarity : 0.004 0.026 561 Dihedral : 6.179 16.376 435 Min Nonbonded Distance : 2.535 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: -1.01 (0.36), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE D 346 TYR 0.008 0.001 TYR B 310 ARG 0.003 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 85 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8331 (mttt) cc_final: 0.7869 (mtpp) REVERT: C 340 LYS cc_start: 0.8559 (mttt) cc_final: 0.8357 (mtpp) REVERT: C 347 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8510 (mtmm) REVERT: C 370 LYS cc_start: 0.8688 (tttt) cc_final: 0.8395 (ttpt) REVERT: A 317 LYS cc_start: 0.8361 (mttt) cc_final: 0.7989 (mtpp) REVERT: A 340 LYS cc_start: 0.8266 (mttt) cc_final: 0.7972 (mtpp) REVERT: D 317 LYS cc_start: 0.8388 (mttt) cc_final: 0.8180 (mttm) REVERT: D 375 LYS cc_start: 0.8736 (tttt) cc_final: 0.8508 (tttt) REVERT: E 317 LYS cc_start: 0.8230 (mttt) cc_final: 0.7625 (mtpp) REVERT: E 340 LYS cc_start: 0.8174 (mttt) cc_final: 0.7864 (mtpp) REVERT: E 345 ASP cc_start: 0.8386 (m-30) cc_final: 0.8094 (t0) REVERT: F 311 LYS cc_start: 0.8659 (mttt) cc_final: 0.7888 (mttm) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 3.3206 time to fit residues: 281.2094 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107521 restraints weight = 12000.014| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.48 r_work: 0.3498 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3297 Z= 0.275 Angle : 0.558 6.032 4410 Z= 0.284 Chirality : 0.051 0.131 495 Planarity : 0.003 0.020 561 Dihedral : 5.533 16.059 435 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.61 % Allowed : 12.90 % Favored : 85.48 % 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: -0.99 (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 C 329 PHE 0.011 0.002 PHE D 346 TYR 0.011 0.002 TYR B 310 ARG 0.003 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 70 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.548 Fit side-chains REVERT: C 317 LYS cc_start: 0.8295 (mttt) cc_final: 0.7834 (mtpp) REVERT: C 340 LYS cc_start: 0.8626 (mttt) cc_final: 0.8415 (mtpp) REVERT: C 347 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: A 317 LYS cc_start: 0.8440 (mttt) cc_final: 0.8029 (mtpp) REVERT: A 340 LYS cc_start: 0.8312 (mttt) cc_final: 0.8022 (mtpp) REVERT: A 345 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8042 (t0) REVERT: E 317 LYS cc_start: 0.8322 (mttt) cc_final: 0.7744 (mtpp) REVERT: E 340 LYS cc_start: 0.8143 (mttt) cc_final: 0.7873 (mtpp) REVERT: E 345 ASP cc_start: 0.8425 (m-30) cc_final: 0.8128 (t0) REVERT: F 311 LYS cc_start: 0.8687 (mttt) cc_final: 0.7922 (mttm) REVERT: F 353 LYS cc_start: 0.8301 (mttt) cc_final: 0.8079 (tttp) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 2.9820 time to fit residues: 204.4642 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS 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 25 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109241 restraints weight = 11914.581| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.47 r_work: 0.3532 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3774 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= 0.136 Angle : 0.496 6.193 4410 Z= 0.249 Chirality : 0.052 0.139 495 Planarity : 0.002 0.018 561 Dihedral : 5.137 15.885 435 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.004 0.001 PHE E 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG D 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 73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8177 (mttt) cc_final: 0.7743 (mtpp) REVERT: C 340 LYS cc_start: 0.8616 (mttt) cc_final: 0.8404 (mtpp) REVERT: C 347 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8583 (mtmm) REVERT: A 317 LYS cc_start: 0.8500 (mttt) cc_final: 0.8117 (mtpp) REVERT: A 340 LYS cc_start: 0.8283 (mttt) cc_final: 0.8002 (mtpp) REVERT: A 345 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8058 (t70) REVERT: E 317 LYS cc_start: 0.8255 (mttt) cc_final: 0.7664 (mtpp) REVERT: E 340 LYS cc_start: 0.8111 (mttt) cc_final: 0.7826 (mtpt) REVERT: E 345 ASP cc_start: 0.8431 (m-30) cc_final: 0.8173 (t0) REVERT: F 311 LYS cc_start: 0.8628 (mttt) cc_final: 0.7853 (mttm) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 2.8330 time to fit residues: 200.0686 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 : 0.524 ------------------------------------------------------------------------------- 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 311 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.0050 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.0170 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.110924 restraints weight = 11866.951| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.46 r_work: 0.3560 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3969 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= 0.132 Angle : 0.468 5.562 4410 Z= 0.234 Chirality : 0.051 0.131 495 Planarity : 0.002 0.019 561 Dihedral : 4.746 15.059 435 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.15 % Allowed : 13.44 % 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: -0.85 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (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 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG C 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 72 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: C 317 LYS cc_start: 0.8107 (mttt) cc_final: 0.7649 (mtpp) REVERT: C 340 LYS cc_start: 0.8619 (mttt) cc_final: 0.8415 (mtpp) REVERT: A 317 LYS cc_start: 0.8450 (mttt) cc_final: 0.8106 (mtpm) REVERT: A 340 LYS cc_start: 0.8291 (mttt) cc_final: 0.8005 (mtpp) REVERT: A 342 GLU cc_start: 0.8037 (tt0) cc_final: 0.7740 (tt0) REVERT: A 345 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (t0) REVERT: E 317 LYS cc_start: 0.8272 (mttt) cc_final: 0.7694 (mtpp) REVERT: E 340 LYS cc_start: 0.8098 (mttt) cc_final: 0.7790 (mtpt) REVERT: E 345 ASP cc_start: 0.8363 (m-30) cc_final: 0.8126 (t0) REVERT: F 311 LYS cc_start: 0.8565 (mttt) cc_final: 0.7806 (mttm) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 3.0808 time to fit residues: 217.3182 Evaluate side-chains 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.120640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111539 restraints weight = 11756.806| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.43 r_work: 0.3566 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4164 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= 0.125 Angle : 0.453 5.339 4410 Z= 0.226 Chirality : 0.052 0.134 495 Planarity : 0.003 0.027 561 Dihedral : 4.542 12.982 435 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.61 % Allowed : 14.78 % 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: -0.81 (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 HIS 0.003 0.000 HIS D 374 PHE 0.004 0.001 PHE E 346 TYR 0.007 0.001 TYR B 310 ARG 0.003 0.000 ARG B 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 73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.545 Fit side-chains REVERT: C 317 LYS cc_start: 0.8084 (mttt) cc_final: 0.7642 (mtpp) REVERT: C 347 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8495 (mttm) REVERT: A 317 LYS cc_start: 0.8424 (mttt) cc_final: 0.8091 (mtpm) REVERT: A 340 LYS cc_start: 0.8306 (mttt) cc_final: 0.8017 (mtpp) REVERT: A 342 GLU cc_start: 0.8043 (tt0) cc_final: 0.7734 (tt0) REVERT: A 345 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8050 (t0) REVERT: E 317 LYS cc_start: 0.8269 (mttt) cc_final: 0.7699 (mtpp) REVERT: E 340 LYS cc_start: 0.8089 (mttt) cc_final: 0.7796 (mtpt) REVERT: E 345 ASP cc_start: 0.8376 (m-30) cc_final: 0.8147 (t0) REVERT: F 311 LYS cc_start: 0.8560 (mttt) cc_final: 0.7795 (mttm) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 3.1158 time to fit residues: 222.9210 Evaluate side-chains 67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.0030 chunk 16 optimal weight: 0.4980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.122501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113309 restraints weight = 11745.901| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.45 r_work: 0.3584 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4333 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= 0.116 Angle : 0.460 5.137 4410 Z= 0.226 Chirality : 0.052 0.131 495 Planarity : 0.003 0.032 561 Dihedral : 4.364 12.135 435 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.45 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 (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: -0.81 (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 HIS 0.002 0.000 HIS D 374 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.001 TYR B 310 ARG 0.002 0.000 ARG B 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 71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.834 Fit side-chains REVERT: A 317 LYS cc_start: 0.8379 (mttt) cc_final: 0.8056 (mtpm) REVERT: A 340 LYS cc_start: 0.8339 (mttt) cc_final: 0.8034 (mtpp) REVERT: A 342 GLU cc_start: 0.8058 (tt0) cc_final: 0.7697 (tt0) REVERT: A 345 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8027 (t0) REVERT: E 317 LYS cc_start: 0.8236 (mttt) cc_final: 0.7695 (mtpp) REVERT: E 340 LYS cc_start: 0.8034 (mttt) cc_final: 0.7737 (mtpt) REVERT: E 345 ASP cc_start: 0.8377 (m-30) cc_final: 0.8155 (t0) REVERT: F 311 LYS cc_start: 0.8546 (mttt) cc_final: 0.7788 (mttm) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 2.9652 time to fit residues: 206.4952 Evaluate side-chains 68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 overall best weight: 1.9794 ------------------------------------------------------------------------------- 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 336 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109058 restraints weight = 12067.927| |-----------------------------------------------------------------------------| r_work (start): 0.3614 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: 2.78 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4387 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= 0.198 Angle : 0.472 4.674 4410 Z= 0.236 Chirality : 0.050 0.127 495 Planarity : 0.003 0.035 561 Dihedral : 4.447 11.478 435 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 : 1.34 % Allowed : 16.40 % 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 (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: -0.79 (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 HIS 0.001 0.000 HIS F 374 PHE 0.007 0.001 PHE F 346 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG C 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 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.537 Fit side-chains REVERT: C 347 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8405 (mptt) REVERT: A 317 LYS cc_start: 0.8404 (mttt) cc_final: 0.8078 (mtpm) REVERT: A 340 LYS cc_start: 0.8331 (mttt) cc_final: 0.8011 (mtpp) REVERT: A 345 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8050 (t70) REVERT: E 317 LYS cc_start: 0.8247 (mttt) cc_final: 0.7729 (mtpp) REVERT: E 340 LYS cc_start: 0.8113 (mttt) cc_final: 0.7799 (mtpt) REVERT: F 311 LYS cc_start: 0.8634 (mttt) cc_final: 0.7860 (mttm) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 3.2280 time to fit residues: 204.4510 Evaluate side-chains 63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.119872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110836 restraints weight = 11995.086| |-----------------------------------------------------------------------------| 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: 0.8764 moved from start: 0.4471 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= 0.120 Angle : 0.454 4.524 4410 Z= 0.225 Chirality : 0.051 0.130 495 Planarity : 0.003 0.036 561 Dihedral : 4.282 11.186 435 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.08 % Allowed : 16.94 % 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 (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: -0.75 (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 0.001 0.000 HIS D 374 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG B 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 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.629 Fit side-chains REVERT: A 317 LYS cc_start: 0.8430 (mttt) cc_final: 0.8087 (mtpm) REVERT: A 340 LYS cc_start: 0.8321 (mttt) cc_final: 0.7992 (mtpp) REVERT: A 345 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8043 (t0) REVERT: E 317 LYS cc_start: 0.8229 (mttt) cc_final: 0.7726 (mtpp) REVERT: E 340 LYS cc_start: 0.8086 (mttt) cc_final: 0.7778 (mtpt) REVERT: F 311 LYS cc_start: 0.8611 (mttt) cc_final: 0.7835 (mttm) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 3.2258 time to fit residues: 208.0178 Evaluate side-chains 64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 0 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109912 restraints weight = 12099.468| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.45 r_work: 0.3537 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3297 Z= 0.167 Angle : 0.454 4.370 4410 Z= 0.226 Chirality : 0.051 0.127 495 Planarity : 0.003 0.040 561 Dihedral : 4.286 10.866 435 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.34 % Allowed : 16.67 % 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 (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: -0.73 (0.39), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (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 0.008 0.002 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 65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.604 Fit side-chains REVERT: A 311 LYS cc_start: 0.8737 (pttt) cc_final: 0.7702 (tppt) REVERT: A 317 LYS cc_start: 0.8433 (mttt) cc_final: 0.8100 (mtpm) REVERT: A 340 LYS cc_start: 0.8359 (mttt) cc_final: 0.8029 (mtpp) REVERT: A 345 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8050 (t0) REVERT: E 317 LYS cc_start: 0.8268 (mttt) cc_final: 0.7783 (mtpp) REVERT: E 340 LYS cc_start: 0.8098 (mttt) cc_final: 0.7789 (mtpt) REVERT: F 311 LYS cc_start: 0.8631 (mttt) cc_final: 0.7850 (mttm) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 3.2211 time to fit residues: 207.4300 Evaluate side-chains 62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 12 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 4 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 = 0.3785 r_free = 0.3785 target = 0.120026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111002 restraints weight = 11980.188| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.45 r_work: 0.3551 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4570 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= 0.123 Angle : 0.449 4.219 4410 Z= 0.222 Chirality : 0.051 0.130 495 Planarity : 0.003 0.042 561 Dihedral : 4.147 11.077 435 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.08 % Allowed : 16.94 % 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 (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 (0.39), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 330 PHE 0.003 0.001 PHE F 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6601.66 seconds wall clock time: 112 minutes 23.89 seconds (6743.89 seconds total)