Starting phenix.real_space_refine on Fri Oct 10 15:22:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q2k_18111/10_2025/8q2k_18111.map" } resolution = 2.88 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= 0.004 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.71, per 1000 atoms: 0.24 Number of scatterers: 7032 At special positions: 0 Unit cell: (132.314, 111.958, 41.439, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 0.64 Conformation dependent library (CDL) restraints added in 301.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.525A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.849A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.474A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.690A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.529A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.382A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.399A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.427A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.654A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.561A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.884A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.512A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (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: 6.664A 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: 6.404A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.565A 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: 6.606A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.477A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.756A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 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: 1.47 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.46: 1059 1.46 - 1.64: 1869 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N ARG D 349 " pdb=" H ARG D 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 HIS F 374 " pdb=" HE1 HIS F 374 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLU B 372 " pdb=" H GLU B 372 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS F 362 " pdb=" HD2 HIS F 362 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" ND1 HIS C 362 " pdb=" HD1 HIS C 362 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11064 2.63 - 5.27: 1456 5.27 - 7.90: 377 7.90 - 10.54: 9 10.54 - 13.17: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.61 6.59 1.30e+00 5.92e-01 2.57e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.64 6.56 1.30e+00 5.92e-01 2.55e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta sigma weight residual 122.37 129.17 -6.80 1.54e+00 4.22e-01 1.95e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 2914 15.15 - 30.31: 169 30.31 - 45.46: 69 45.46 - 60.61: 66 60.61 - 75.76: 46 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA GLN A 307 " pdb=" C GLN A 307 " pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" C LYS F 343 " pdb=" N LYS F 343 " pdb=" CA LYS F 343 " pdb=" CB LYS F 343 " ideal model delta harmonic sigma weight residual -122.60 -130.95 8.35 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA THR F 319 " pdb=" C THR F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 242 0.050 - 0.099: 214 0.099 - 0.148: 57 0.148 - 0.197: 12 0.197 - 0.246: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LYS E 331 " pdb=" N LYS E 331 " pdb=" C LYS E 331 " pdb=" CB LYS E 331 " 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 E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 374 " -0.095 2.00e-02 2.50e+03 5.49e-02 6.77e+01 pdb=" CG HIS D 374 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS D 374 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS D 374 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS D 374 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS D 374 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS D 374 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS D 374 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 HIS D 374 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.086 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.089 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS C 374 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.085 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 603 2.18 - 2.79: 12295 2.79 - 3.39: 18077 3.39 - 4.00: 25062 4.00 - 4.60: 34061 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.588 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.591 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.627 2.450 ... (remaining 90093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 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: 0.040 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.034 3498 Z= 0.691 Angle : 1.799 6.798 4680 Z= 1.181 Chirality : 0.070 0.246 528 Planarity : 0.009 0.040 594 Dihedral : 10.493 67.213 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.81 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.046 0.009 TYR E 310 PHE 0.057 0.020 PHE C 346 HIS 0.014 0.004 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.01110 ( 3498) covalent geometry : angle 1.79874 ( 4680) hydrogen bonds : bond 0.04515 ( 86) hydrogen bonds : angle 7.15309 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6833 (tt0) cc_final: 0.6070 (tp30) REVERT: A 345 ASP cc_start: 0.7509 (t0) cc_final: 0.7099 (m-30) REVERT: A 353 LYS cc_start: 0.6953 (mttt) cc_final: 0.6643 (tmtp) REVERT: A 369 LYS cc_start: 0.6927 (tttt) cc_final: 0.6665 (ttpt) REVERT: B 336 GLN cc_start: 0.8112 (tt0) cc_final: 0.7902 (tt0) REVERT: B 338 GLU cc_start: 0.7620 (tt0) cc_final: 0.7358 (tt0) REVERT: B 340 LYS cc_start: 0.7237 (tttt) cc_final: 0.6328 (tmtm) REVERT: B 342 GLU cc_start: 0.7244 (tt0) cc_final: 0.6922 (tt0) REVERT: B 358 ASP cc_start: 0.7535 (m-30) cc_final: 0.7163 (m-30) REVERT: C 317 LYS cc_start: 0.7883 (mttt) cc_final: 0.7527 (mtpt) REVERT: C 338 GLU cc_start: 0.7478 (tt0) cc_final: 0.6733 (tp30) REVERT: C 353 LYS cc_start: 0.7589 (mttt) cc_final: 0.7178 (tmtp) REVERT: D 331 LYS cc_start: 0.7713 (mttt) cc_final: 0.7218 (mmmt) REVERT: D 336 GLN cc_start: 0.8535 (tt0) cc_final: 0.8327 (tt0) REVERT: D 340 LYS cc_start: 0.8070 (tttt) cc_final: 0.7305 (tptt) REVERT: D 342 GLU cc_start: 0.7679 (tt0) cc_final: 0.7387 (tt0) REVERT: D 347 LYS cc_start: 0.7856 (mttt) cc_final: 0.7487 (mmtm) REVERT: D 353 LYS cc_start: 0.7654 (mttt) cc_final: 0.7375 (tttm) REVERT: E 311 LYS cc_start: 0.6760 (mttt) cc_final: 0.5684 (mmtt) REVERT: E 338 GLU cc_start: 0.6683 (tt0) cc_final: 0.6004 (tp30) REVERT: E 345 ASP cc_start: 0.7525 (t0) cc_final: 0.7205 (m-30) REVERT: E 353 LYS cc_start: 0.6974 (mttt) cc_final: 0.6665 (tttm) REVERT: E 369 LYS cc_start: 0.7106 (tttt) cc_final: 0.6522 (ttmp) REVERT: F 311 LYS cc_start: 0.7287 (mttt) cc_final: 0.6020 (mmtt) REVERT: F 338 GLU cc_start: 0.7409 (tt0) cc_final: 0.7025 (tm-30) REVERT: F 340 LYS cc_start: 0.7381 (tttt) cc_final: 0.6549 (tptt) REVERT: F 349 ARG cc_start: 0.5764 (mtm180) cc_final: 0.5084 (mmp80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 1.9831 time to fit residues: 249.9198 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.148237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.139473 restraints weight = 14436.932| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.35 r_work: 0.3905 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3498 Z= 0.118 Angle : 0.528 4.334 4680 Z= 0.276 Chirality : 0.050 0.133 528 Planarity : 0.004 0.034 594 Dihedral : 5.377 13.180 462 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.005 0.001 TYR C 310 PHE 0.006 0.001 PHE B 346 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3498) covalent geometry : angle 0.52816 ( 4680) hydrogen bonds : bond 0.01740 ( 86) hydrogen bonds : angle 4.97973 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.199 Fit side-chains REVERT: A 338 GLU cc_start: 0.7576 (tt0) cc_final: 0.7243 (tp30) REVERT: A 351 GLN cc_start: 0.8208 (tt0) cc_final: 0.7891 (tt0) REVERT: A 369 LYS cc_start: 0.8204 (tttt) cc_final: 0.7974 (ttmp) REVERT: B 340 LYS cc_start: 0.7989 (tttt) cc_final: 0.7617 (tmtm) REVERT: B 342 GLU cc_start: 0.7629 (tt0) cc_final: 0.7415 (tt0) REVERT: C 338 GLU cc_start: 0.7556 (tt0) cc_final: 0.7251 (tp30) REVERT: C 347 LYS cc_start: 0.8698 (mppt) cc_final: 0.8496 (mptp) REVERT: C 349 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.5738 (mtt90) REVERT: C 351 GLN cc_start: 0.8429 (tt0) cc_final: 0.8142 (tt0) REVERT: D 336 GLN cc_start: 0.8630 (tt0) cc_final: 0.8423 (tt0) REVERT: D 340 LYS cc_start: 0.8403 (tttt) cc_final: 0.8100 (tptt) REVERT: D 349 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.4639 (pmt-80) REVERT: E 311 LYS cc_start: 0.7595 (mttt) cc_final: 0.6637 (mmtm) REVERT: E 317 LYS cc_start: 0.8154 (mttt) cc_final: 0.7901 (ttmm) REVERT: E 338 GLU cc_start: 0.7606 (tt0) cc_final: 0.7244 (tp30) REVERT: E 369 LYS cc_start: 0.8384 (tttt) cc_final: 0.8016 (ttmp) REVERT: F 340 LYS cc_start: 0.7966 (tttt) cc_final: 0.7640 (tptt) REVERT: F 349 ARG cc_start: 0.6815 (mtm180) cc_final: 0.6087 (mmp80) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 1.8045 time to fit residues: 165.3582 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain F residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.140260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131735 restraints weight = 14862.358| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.35 r_work: 0.3809 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.162 Angle : 0.520 4.396 4680 Z= 0.266 Chirality : 0.050 0.129 528 Planarity : 0.004 0.030 594 Dihedral : 4.898 12.363 462 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 16.41 % Favored : 82.07 % 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: -1.60 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.007 0.001 TYR C 310 PHE 0.008 0.002 PHE E 346 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3498) covalent geometry : angle 0.51972 ( 4680) hydrogen bonds : bond 0.01771 ( 86) hydrogen bonds : angle 4.44432 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.208 Fit side-chains REVERT: A 338 GLU cc_start: 0.7698 (tt0) cc_final: 0.7318 (tp30) REVERT: A 351 GLN cc_start: 0.8297 (tt0) cc_final: 0.7988 (tt0) REVERT: B 340 LYS cc_start: 0.8036 (tttt) cc_final: 0.7608 (tmtm) REVERT: B 342 GLU cc_start: 0.7671 (tt0) cc_final: 0.7447 (tt0) REVERT: C 338 GLU cc_start: 0.7635 (tt0) cc_final: 0.7326 (tp30) REVERT: C 349 ARG cc_start: 0.6926 (mtm-85) cc_final: 0.5656 (mtt90) REVERT: D 340 LYS cc_start: 0.8375 (tttt) cc_final: 0.8024 (tptt) REVERT: D 349 ARG cc_start: 0.6936 (mtm-85) cc_final: 0.4520 (pmt-80) REVERT: E 317 LYS cc_start: 0.8186 (mttt) cc_final: 0.7888 (ttmm) REVERT: E 338 GLU cc_start: 0.7657 (tt0) cc_final: 0.7294 (tp30) REVERT: F 340 LYS cc_start: 0.7984 (tttt) cc_final: 0.7622 (tptt) REVERT: F 349 ARG cc_start: 0.6920 (mtm180) cc_final: 0.6079 (mmp80) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 1.6860 time to fit residues: 115.2940 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134897 restraints weight = 14907.208| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.37 r_work: 0.3865 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.098 Angle : 0.465 4.195 4680 Z= 0.233 Chirality : 0.050 0.128 528 Planarity : 0.003 0.023 594 Dihedral : 4.430 11.548 462 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 17.93 % Favored : 80.81 % 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: -1.42 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.006 0.001 TYR C 310 PHE 0.004 0.001 PHE B 378 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 3498) covalent geometry : angle 0.46460 ( 4680) hydrogen bonds : bond 0.01367 ( 86) hydrogen bonds : angle 4.04727 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7703 (tt0) cc_final: 0.7295 (tp30) REVERT: A 351 GLN cc_start: 0.8226 (tt0) cc_final: 0.7980 (tt0) REVERT: B 340 LYS cc_start: 0.7953 (tttt) cc_final: 0.7567 (tmtm) REVERT: B 342 GLU cc_start: 0.7676 (tt0) cc_final: 0.7462 (tt0) REVERT: C 338 GLU cc_start: 0.7570 (tt0) cc_final: 0.7258 (tp30) REVERT: D 340 LYS cc_start: 0.8352 (tttt) cc_final: 0.8014 (tptt) REVERT: E 317 LYS cc_start: 0.8161 (mttt) cc_final: 0.7897 (tttp) REVERT: E 338 GLU cc_start: 0.7606 (tt0) cc_final: 0.7268 (tp30) REVERT: F 340 LYS cc_start: 0.7904 (tttt) cc_final: 0.7578 (tptt) REVERT: F 349 ARG cc_start: 0.6892 (mtm180) cc_final: 0.6050 (mmp80) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 1.5448 time to fit residues: 101.1684 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.133463 restraints weight = 14869.736| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.36 r_work: 0.3849 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.115 Angle : 0.465 4.176 4680 Z= 0.233 Chirality : 0.050 0.128 528 Planarity : 0.003 0.022 594 Dihedral : 4.291 11.559 462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.81 % 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: -1.42 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.008 0.001 TYR A 310 PHE 0.005 0.001 PHE A 378 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3498) covalent geometry : angle 0.46539 ( 4680) hydrogen bonds : bond 0.01437 ( 86) hydrogen bonds : angle 3.85895 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.278 Fit side-chains REVERT: A 351 GLN cc_start: 0.8273 (tt0) cc_final: 0.8037 (tt0) REVERT: A 358 ASP cc_start: 0.8194 (m-30) cc_final: 0.7989 (m-30) REVERT: B 340 LYS cc_start: 0.7993 (tttt) cc_final: 0.7594 (tmtm) REVERT: B 342 GLU cc_start: 0.7670 (tt0) cc_final: 0.7465 (tt0) REVERT: C 338 GLU cc_start: 0.7596 (tt0) cc_final: 0.7286 (tp30) REVERT: C 358 ASP cc_start: 0.8401 (m-30) cc_final: 0.8195 (m-30) REVERT: D 340 LYS cc_start: 0.8382 (tttt) cc_final: 0.8026 (tptt) REVERT: E 317 LYS cc_start: 0.8200 (mttt) cc_final: 0.7936 (tttp) REVERT: E 338 GLU cc_start: 0.7626 (tt0) cc_final: 0.7303 (tp30) REVERT: E 351 GLN cc_start: 0.8477 (tt0) cc_final: 0.8067 (tt0) REVERT: F 340 LYS cc_start: 0.7894 (tttt) cc_final: 0.7581 (tptt) REVERT: F 349 ARG cc_start: 0.6942 (mtm180) cc_final: 0.6047 (mmp80) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 1.4589 time to fit residues: 94.2704 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.130284 restraints weight = 14756.434| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.32 r_work: 0.3794 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.209 Angle : 0.511 4.461 4680 Z= 0.261 Chirality : 0.049 0.124 528 Planarity : 0.004 0.026 594 Dihedral : 4.596 12.178 462 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 19.70 % Favored : 78.79 % 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: -1.69 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.006 0.001 TYR E 310 PHE 0.010 0.002 PHE A 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3498) covalent geometry : angle 0.51129 ( 4680) hydrogen bonds : bond 0.01767 ( 86) hydrogen bonds : angle 4.11114 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.218 Fit side-chains REVERT: A 345 ASP cc_start: 0.8242 (m-30) cc_final: 0.8042 (m-30) REVERT: A 351 GLN cc_start: 0.8404 (tt0) cc_final: 0.8146 (tt0) REVERT: B 340 LYS cc_start: 0.8059 (tttt) cc_final: 0.7640 (tmtm) REVERT: C 338 GLU cc_start: 0.7656 (tt0) cc_final: 0.7338 (tp30) REVERT: C 349 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.5848 (mtt90) REVERT: D 340 LYS cc_start: 0.8386 (tttt) cc_final: 0.8010 (tptt) REVERT: D 349 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.4578 (pmt-80) REVERT: E 317 LYS cc_start: 0.8201 (mttt) cc_final: 0.7876 (ttmm) REVERT: E 338 GLU cc_start: 0.7650 (tt0) cc_final: 0.7311 (tp30) REVERT: E 351 GLN cc_start: 0.8509 (tt0) cc_final: 0.8199 (tt0) REVERT: F 340 LYS cc_start: 0.7942 (tttt) cc_final: 0.7603 (tptt) REVERT: F 349 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6038 (mmp80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 1.4366 time to fit residues: 91.2358 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132792 restraints weight = 14919.516| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.36 r_work: 0.3843 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.096 Angle : 0.452 4.119 4680 Z= 0.227 Chirality : 0.050 0.124 528 Planarity : 0.003 0.024 594 Dihedral : 4.148 11.349 462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 20.45 % Favored : 78.79 % 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: -1.63 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.006 0.001 TYR A 310 PHE 0.003 0.001 PHE B 378 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 3498) covalent geometry : angle 0.45232 ( 4680) hydrogen bonds : bond 0.01363 ( 86) hydrogen bonds : angle 3.81098 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.222 Fit side-chains REVERT: A 351 GLN cc_start: 0.8263 (tt0) cc_final: 0.8034 (tt0) REVERT: B 340 LYS cc_start: 0.7964 (tttt) cc_final: 0.7587 (tmtm) REVERT: C 338 GLU cc_start: 0.7589 (tt0) cc_final: 0.7277 (tp30) REVERT: D 340 LYS cc_start: 0.8393 (tttt) cc_final: 0.8025 (tptt) REVERT: E 317 LYS cc_start: 0.8187 (mttt) cc_final: 0.7930 (tttp) REVERT: E 338 GLU cc_start: 0.7586 (tt0) cc_final: 0.7261 (tp30) REVERT: E 351 GLN cc_start: 0.8459 (tt0) cc_final: 0.8111 (tt0) REVERT: F 340 LYS cc_start: 0.7900 (tttt) cc_final: 0.7594 (tptt) REVERT: F 349 ARG cc_start: 0.7036 (mtm180) cc_final: 0.6059 (mmp80) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 1.5384 time to fit residues: 91.3059 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 0.0000 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.143708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.135708 restraints weight = 14926.150| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.37 r_work: 0.3881 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.077 Angle : 0.435 3.935 4680 Z= 0.215 Chirality : 0.051 0.126 528 Planarity : 0.003 0.023 594 Dihedral : 3.828 10.293 462 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 20.71 % Favored : 78.54 % 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: -1.47 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.007 0.001 TYR A 310 PHE 0.003 0.001 PHE E 346 HIS 0.001 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 3498) covalent geometry : angle 0.43533 ( 4680) hydrogen bonds : bond 0.01218 ( 86) hydrogen bonds : angle 3.62942 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.7981 (tttt) cc_final: 0.7590 (tmtm) REVERT: C 338 GLU cc_start: 0.7561 (tt0) cc_final: 0.7253 (tp30) REVERT: D 340 LYS cc_start: 0.8395 (tttt) cc_final: 0.8039 (tptt) REVERT: E 317 LYS cc_start: 0.8173 (mttt) cc_final: 0.7931 (tttp) REVERT: E 338 GLU cc_start: 0.7592 (tt0) cc_final: 0.7279 (tp30) REVERT: E 351 GLN cc_start: 0.8455 (tt0) cc_final: 0.8120 (tt0) REVERT: F 340 LYS cc_start: 0.7882 (tttt) cc_final: 0.7568 (tptt) REVERT: F 349 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6084 (mmp80) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 1.4995 time to fit residues: 96.7794 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132284 restraints weight = 14738.576| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.33 r_work: 0.3837 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.140 Angle : 0.461 4.171 4680 Z= 0.232 Chirality : 0.050 0.126 528 Planarity : 0.003 0.026 594 Dihedral : 4.121 11.610 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.76 % Allowed : 22.22 % Favored : 77.02 % 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: -1.67 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.004 0.001 TYR B 310 PHE 0.006 0.001 PHE A 378 HIS 0.002 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3498) covalent geometry : angle 0.46077 ( 4680) hydrogen bonds : bond 0.01522 ( 86) hydrogen bonds : angle 3.80786 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.218 Fit side-chains REVERT: B 340 LYS cc_start: 0.8047 (tttt) cc_final: 0.7634 (tmtm) REVERT: C 338 GLU cc_start: 0.7597 (tt0) cc_final: 0.7299 (tp30) REVERT: C 349 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.5992 (mtt90) REVERT: D 340 LYS cc_start: 0.8396 (tttt) cc_final: 0.8016 (tptt) REVERT: D 349 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.4615 (pmt-80) REVERT: E 317 LYS cc_start: 0.8180 (mttt) cc_final: 0.7887 (ttmm) REVERT: E 338 GLU cc_start: 0.7619 (tt0) cc_final: 0.7295 (tp30) REVERT: E 351 GLN cc_start: 0.8465 (tt0) cc_final: 0.8138 (tt0) REVERT: F 340 LYS cc_start: 0.7935 (tttt) cc_final: 0.7601 (tptt) REVERT: F 349 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6094 (mmp80) outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 1.5773 time to fit residues: 93.6293 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.139906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131660 restraints weight = 14810.217| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.35 r_work: 0.3827 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.138 Angle : 0.463 4.237 4680 Z= 0.234 Chirality : 0.050 0.124 528 Planarity : 0.003 0.027 594 Dihedral : 4.212 11.746 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.51 % Allowed : 22.22 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.76 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.005 0.001 TYR C 310 PHE 0.006 0.001 PHE A 378 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3498) covalent geometry : angle 0.46346 ( 4680) hydrogen bonds : bond 0.01574 ( 86) hydrogen bonds : angle 3.89397 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.215 Fit side-chains REVERT: B 340 LYS cc_start: 0.8061 (tttt) cc_final: 0.7651 (tmtm) REVERT: C 338 GLU cc_start: 0.7588 (tt0) cc_final: 0.7295 (tp30) REVERT: C 349 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.6034 (mtt90) REVERT: D 340 LYS cc_start: 0.8400 (tttt) cc_final: 0.8018 (tptt) REVERT: D 349 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.4611 (pmt-80) REVERT: E 317 LYS cc_start: 0.8178 (mttt) cc_final: 0.7906 (tttp) REVERT: E 338 GLU cc_start: 0.7605 (tt0) cc_final: 0.7290 (tp30) REVERT: E 351 GLN cc_start: 0.8468 (tt0) cc_final: 0.8176 (tt0) REVERT: F 340 LYS cc_start: 0.7926 (tttt) cc_final: 0.7607 (tptt) REVERT: F 349 ARG cc_start: 0.7117 (mtm180) cc_final: 0.6072 (mmp80) REVERT: F 372 GLU cc_start: 0.7690 (tt0) cc_final: 0.7482 (tp30) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 1.5691 time to fit residues: 89.9522 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.131882 restraints weight = 14584.970| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.33 r_work: 0.3822 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.134 Angle : 0.461 4.202 4680 Z= 0.232 Chirality : 0.050 0.123 528 Planarity : 0.003 0.027 594 Dihedral : 4.158 11.649 462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.76 % Allowed : 22.47 % Favored : 76.77 % 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: -1.81 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.005 0.001 TYR C 310 PHE 0.006 0.001 PHE A 378 HIS 0.002 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3498) covalent geometry : angle 0.46135 ( 4680) hydrogen bonds : bond 0.01561 ( 86) hydrogen bonds : angle 3.88670 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.06 seconds wall clock time: 56 minutes 59.80 seconds (3419.80 seconds total)