Starting phenix.real_space_refine on Wed Mar 12 02:30:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q2k_18111/03_2025/8q2k_18111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q2k_18111/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q2k_18111/03_2025/8q2k_18111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q2k_18111/03_2025/8q2k_18111.map" model { file = "/net/cci-nas-00/data/ceres_data/8q2k_18111/03_2025/8q2k_18111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q2k_18111/03_2025/8q2k_18111.cif" } resolution = 2.88 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= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.23, per 1000 atoms: 0.60 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: 1.66 Conformation dependent library (CDL) restraints added in 575.6 milliseconds 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: 0.74 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: 2.10 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: 0.94 - 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: 0.01 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.170 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- 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= 0.750 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 (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: -1.81 (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 HIS 0.014 0.004 HIS B 362 PHE 0.057 0.020 PHE C 346 TYR 0.046 0.009 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) ************************************************ 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 : 0.544 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: A 338 GLU cc_start: 0.6833 (tt0) cc_final: 0.6071 (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: 0.7357 (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 353 LYS cc_start: 0.6929 (mttt) cc_final: 0.6693 (tttm) 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: 0.8326 (tt0) REVERT: D 340 LYS cc_start: 0.8070 (tttt) cc_final: 0.7304 (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: 0.7486 (mmtm) REVERT: D 349 ARG cc_start: 0.6417 (mtm180) cc_final: 0.4258 (pmt-80) REVERT: D 353 LYS cc_start: 0.7654 (mttt) cc_final: 0.7375 (tttm) REVERT: D 358 ASP cc_start: 0.7846 (m-30) cc_final: 0.7598 (m-30) REVERT: E 311 LYS cc_start: 0.6760 (mttt) cc_final: 0.5686 (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: 0.6523 (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: 0.7026 (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: 0.5079 (mmp80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 3.7774 time to fit residues: 476.7920 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.140235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.131264 restraints weight = 14550.913| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.38 r_work: 0.3821 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3498 Z= 0.372 Angle : 0.587 4.710 4680 Z= 0.314 Chirality : 0.050 0.131 528 Planarity : 0.005 0.039 594 Dihedral : 5.582 13.277 462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.26 % Allowed : 11.62 % Favored : 87.12 % 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: -1.77 (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 HIS 0.004 0.002 HIS E 329 PHE 0.011 0.003 PHE E 346 TYR 0.006 0.001 TYR C 310 ARG 0.003 0.001 ARG E 349 *********************** 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 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7708 (tt0) cc_final: 0.7307 (tp30) REVERT: A 369 LYS cc_start: 0.8263 (tttt) cc_final: 0.7974 (ttmp) REVERT: B 340 LYS cc_start: 0.8082 (tttt) cc_final: 0.7608 (tmtm) REVERT: C 338 GLU cc_start: 0.7710 (tt0) cc_final: 0.7350 (tp30) REVERT: C 349 ARG cc_start: 0.7031 (mtm-85) cc_final: 0.5660 (mtt90) REVERT: C 351 GLN cc_start: 0.8566 (tt0) cc_final: 0.8263 (tt0) REVERT: D 340 LYS cc_start: 0.8442 (tttt) cc_final: 0.8036 (tptt) REVERT: D 349 ARG cc_start: 0.7283 (mtm180) cc_final: 0.5100 (pmt-80) REVERT: E 311 LYS cc_start: 0.7869 (mttt) cc_final: 0.6804 (mmtt) REVERT: E 338 GLU cc_start: 0.7675 (tt0) cc_final: 0.7264 (tp30) REVERT: E 369 LYS cc_start: 0.8390 (tttt) cc_final: 0.8057 (ttmp) REVERT: F 340 LYS cc_start: 0.8002 (tttt) cc_final: 0.7631 (tptt) REVERT: F 349 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6052 (mmp80) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 3.7936 time to fit residues: 339.9891 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.141574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133086 restraints weight = 14868.622| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.39 r_work: 0.3834 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4464 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= 0.184 Angle : 0.495 4.380 4680 Z= 0.252 Chirality : 0.050 0.133 528 Planarity : 0.004 0.030 594 Dihedral : 4.779 12.160 462 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 16.16 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE C 378 TYR 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7704 (tt0) cc_final: 0.7319 (tp30) REVERT: A 351 GLN cc_start: 0.8433 (tt0) cc_final: 0.8118 (tt0) REVERT: B 340 LYS cc_start: 0.8023 (tttt) cc_final: 0.7608 (tmtm) REVERT: C 338 GLU cc_start: 0.7599 (tt0) cc_final: 0.7292 (tp30) REVERT: C 349 ARG cc_start: 0.6873 (mtm-85) cc_final: 0.5644 (mtt90) REVERT: D 340 LYS cc_start: 0.8372 (tttt) cc_final: 0.8025 (tptt) REVERT: E 338 GLU cc_start: 0.7629 (tt0) cc_final: 0.7279 (tp30) REVERT: F 340 LYS cc_start: 0.7988 (tttt) cc_final: 0.7675 (tptt) REVERT: F 349 ARG cc_start: 0.6929 (mtm180) cc_final: 0.6091 (mmp80) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 3.5545 time to fit residues: 246.7768 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.9284 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.144526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136237 restraints weight = 14886.099| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.39 r_work: 0.3883 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.118 Angle : 0.452 4.116 4680 Z= 0.226 Chirality : 0.050 0.125 528 Planarity : 0.003 0.021 594 Dihedral : 4.269 10.815 462 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 18.69 % Favored : 80.05 % 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: -1.42 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 330 PHE 0.003 0.001 PHE E 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 379 *********************** 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 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7702 (tt0) cc_final: 0.7290 (tp30) REVERT: A 351 GLN cc_start: 0.8385 (tt0) cc_final: 0.8134 (tt0) REVERT: B 340 LYS cc_start: 0.7948 (tttt) cc_final: 0.7567 (tmtm) REVERT: C 338 GLU cc_start: 0.7571 (tt0) cc_final: 0.7264 (tp30) REVERT: D 340 LYS cc_start: 0.8367 (tttt) cc_final: 0.8000 (tptt) REVERT: E 317 LYS cc_start: 0.8194 (mttt) cc_final: 0.7945 (tttp) REVERT: E 338 GLU cc_start: 0.7645 (tt0) cc_final: 0.7259 (tp30) REVERT: E 351 GLN cc_start: 0.8489 (tt0) cc_final: 0.8122 (tt0) REVERT: F 340 LYS cc_start: 0.7891 (tttt) cc_final: 0.7568 (tptt) REVERT: F 349 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6050 (mmp80) outliers start: 5 outliers final: 1 residues processed: 64 average time/residue: 2.9561 time to fit residues: 193.9449 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.144343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136237 restraints weight = 14687.937| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.33 r_work: 0.3883 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.002 0.020 3498 Z= 0.128 Angle : 0.440 4.065 4680 Z= 0.220 Chirality : 0.050 0.124 528 Planarity : 0.003 0.021 594 Dihedral : 4.075 10.769 462 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 18.18 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 330 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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: 5 poor density : 60 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7682 (tt0) cc_final: 0.7295 (tp30) REVERT: A 351 GLN cc_start: 0.8395 (tt0) cc_final: 0.8189 (tt0) REVERT: B 340 LYS cc_start: 0.7972 (tttt) cc_final: 0.7611 (tmtm) REVERT: C 338 GLU cc_start: 0.7532 (tt0) cc_final: 0.7258 (tp30) REVERT: D 340 LYS cc_start: 0.8353 (tttt) cc_final: 0.8013 (tptt) REVERT: E 317 LYS cc_start: 0.8155 (mttt) cc_final: 0.7953 (tttp) REVERT: E 338 GLU cc_start: 0.7628 (tt0) cc_final: 0.7302 (tp30) REVERT: E 351 GLN cc_start: 0.8477 (tt0) cc_final: 0.8149 (tt0) REVERT: F 340 LYS cc_start: 0.7872 (tttt) cc_final: 0.7578 (tptt) REVERT: F 349 ARG cc_start: 0.6949 (mtm180) cc_final: 0.6069 (mmp80) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 2.7543 time to fit residues: 181.0551 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 : 0.585 ------------------------------------------------------------------------------- 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 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134141 restraints weight = 14620.074| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.34 r_work: 0.3841 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.162 Angle : 0.451 4.121 4680 Z= 0.226 Chirality : 0.050 0.123 528 Planarity : 0.003 0.023 594 Dihedral : 4.147 11.413 462 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.26 % Allowed : 18.94 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.005 0.001 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7651 (tt0) cc_final: 0.7283 (tp30) REVERT: A 351 GLN cc_start: 0.8413 (tt0) cc_final: 0.8195 (tt0) REVERT: B 340 LYS cc_start: 0.8023 (tttt) cc_final: 0.7628 (tmtm) REVERT: C 338 GLU cc_start: 0.7546 (tt0) cc_final: 0.7268 (tp30) REVERT: D 340 LYS cc_start: 0.8383 (tttt) cc_final: 0.8008 (tptt) REVERT: E 317 LYS cc_start: 0.8189 (mttt) cc_final: 0.7911 (tttp) REVERT: E 338 GLU cc_start: 0.7624 (tt0) cc_final: 0.7289 (tp30) REVERT: E 351 GLN cc_start: 0.8488 (tt0) cc_final: 0.8205 (tt0) REVERT: F 340 LYS cc_start: 0.7914 (tttt) cc_final: 0.7585 (tptt) REVERT: F 349 ARG cc_start: 0.7000 (mtm180) cc_final: 0.6124 (mmp80) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 2.8495 time to fit residues: 175.5156 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 : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER 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 32 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.138860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130414 restraints weight = 14528.584| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.33 r_work: 0.3797 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.291 Angle : 0.500 4.397 4680 Z= 0.256 Chirality : 0.049 0.126 528 Planarity : 0.004 0.028 594 Dihedral : 4.515 12.237 462 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.78 % Allowed : 18.69 % 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 (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: -1.78 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.001 ARG D 379 *********************** 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 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8041 (mttt) cc_final: 0.7585 (mtpt) REVERT: A 338 GLU cc_start: 0.7685 (tt0) cc_final: 0.7268 (tp30) REVERT: A 351 GLN cc_start: 0.8516 (tt0) cc_final: 0.8226 (tt0) REVERT: B 340 LYS cc_start: 0.8071 (tttt) cc_final: 0.7640 (tmtm) REVERT: C 338 GLU cc_start: 0.7680 (tt0) cc_final: 0.7365 (tp30) REVERT: C 349 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.5851 (mtt90) REVERT: D 340 LYS cc_start: 0.8421 (tttt) cc_final: 0.8009 (tptt) REVERT: D 349 ARG cc_start: 0.7459 (mtm180) cc_final: 0.5118 (pmt-80) REVERT: E 317 LYS cc_start: 0.8203 (mttt) cc_final: 0.7833 (tttp) REVERT: E 338 GLU cc_start: 0.7693 (tt0) cc_final: 0.7349 (tp30) REVERT: E 351 GLN cc_start: 0.8508 (tt0) cc_final: 0.8212 (tt0) REVERT: F 340 LYS cc_start: 0.7939 (tttt) cc_final: 0.7588 (tptt) REVERT: F 349 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6042 (mmp80) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 2.9932 time to fit residues: 208.4343 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.139291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130928 restraints weight = 14796.886| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.34 r_work: 0.3800 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3498 Z= 0.236 Angle : 0.476 4.343 4680 Z= 0.242 Chirality : 0.049 0.122 528 Planarity : 0.003 0.027 594 Dihedral : 4.405 12.101 462 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.52 % Allowed : 19.95 % 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 (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: -1.88 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.007 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.590 Fit side-chains REVERT: A 317 LYS cc_start: 0.8018 (mttt) cc_final: 0.7579 (mtpt) REVERT: A 338 GLU cc_start: 0.7659 (tt0) cc_final: 0.7269 (tp30) REVERT: A 351 GLN cc_start: 0.8496 (tt0) cc_final: 0.8240 (tt0) REVERT: B 340 LYS cc_start: 0.8074 (tttt) cc_final: 0.7661 (tmtm) REVERT: C 338 GLU cc_start: 0.7660 (tt0) cc_final: 0.7355 (tp30) REVERT: C 349 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.5860 (mtt90) REVERT: D 340 LYS cc_start: 0.8415 (tttt) cc_final: 0.8025 (tptt) REVERT: D 349 ARG cc_start: 0.7515 (mtm180) cc_final: 0.5161 (pmt-80) REVERT: E 317 LYS cc_start: 0.8217 (mttt) cc_final: 0.7909 (tttp) REVERT: E 338 GLU cc_start: 0.7668 (tt0) cc_final: 0.7332 (tp30) REVERT: E 351 GLN cc_start: 0.8498 (tt0) cc_final: 0.8220 (tt0) REVERT: F 340 LYS cc_start: 0.7920 (tttt) cc_final: 0.7590 (tptt) REVERT: F 349 ARG cc_start: 0.7094 (mtm180) cc_final: 0.6062 (mmp80) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 3.4179 time to fit residues: 238.1159 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.135422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127308 restraints weight = 15190.351| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.35 r_work: 0.3796 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5243 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= 0.147 Angle : 0.446 4.121 4680 Z= 0.224 Chirality : 0.050 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 4.082 11.198 462 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 21.46 % Favored : 77.53 % 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: -1.74 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.005 0.001 PHE B 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** 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: 4 poor density : 54 time to evaluate : 0.609 Fit side-chains REVERT: A 351 GLN cc_start: 0.8446 (tt0) cc_final: 0.8228 (tt0) REVERT: B 340 LYS cc_start: 0.8040 (tttt) cc_final: 0.7645 (tmtm) REVERT: C 338 GLU cc_start: 0.7565 (tt0) cc_final: 0.7249 (tp30) REVERT: D 340 LYS cc_start: 0.8384 (tttt) cc_final: 0.8007 (tptt) REVERT: E 317 LYS cc_start: 0.8199 (mttt) cc_final: 0.7934 (tttp) REVERT: E 338 GLU cc_start: 0.7617 (tt0) cc_final: 0.7291 (tp30) REVERT: E 351 GLN cc_start: 0.8472 (tt0) cc_final: 0.8198 (tt0) REVERT: F 340 LYS cc_start: 0.7879 (tttt) cc_final: 0.7541 (tptt) REVERT: F 349 ARG cc_start: 0.7110 (mtm180) cc_final: 0.6068 (mmp80) REVERT: F 372 GLU cc_start: 0.7651 (tt0) cc_final: 0.7422 (tp30) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 2.8828 time to fit residues: 168.7086 Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 5 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.133666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125521 restraints weight = 15547.438| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.37 r_work: 0.3749 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.214 Angle : 0.472 4.279 4680 Z= 0.238 Chirality : 0.050 0.123 528 Planarity : 0.003 0.027 594 Dihedral : 4.248 11.892 462 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 21.72 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.007 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG C 379 ********************** 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 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.658 Fit side-chains REVERT: A 351 GLN cc_start: 0.8492 (tt0) cc_final: 0.8253 (tt0) REVERT: B 340 LYS cc_start: 0.8052 (tttt) cc_final: 0.7634 (tmtm) REVERT: C 338 GLU cc_start: 0.7649 (tt0) cc_final: 0.7307 (tp30) REVERT: C 349 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.5955 (mtt90) REVERT: D 340 LYS cc_start: 0.8401 (tttt) cc_final: 0.7999 (tptt) REVERT: D 349 ARG cc_start: 0.7521 (mtm180) cc_final: 0.5151 (pmt-80) REVERT: E 317 LYS cc_start: 0.8219 (mttt) cc_final: 0.7879 (tttp) REVERT: E 338 GLU cc_start: 0.7635 (tt0) cc_final: 0.7314 (tp30) REVERT: E 351 GLN cc_start: 0.8489 (tt0) cc_final: 0.8218 (tt0) REVERT: F 340 LYS cc_start: 0.7921 (tttt) cc_final: 0.7526 (tptt) REVERT: F 349 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6001 (mmp80) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 2.9727 time to fit residues: 179.8942 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.133529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125381 restraints weight = 15328.156| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.37 r_work: 0.3760 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5279 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= 0.202 Angle : 0.468 4.254 4680 Z= 0.235 Chirality : 0.050 0.123 528 Planarity : 0.003 0.026 594 Dihedral : 4.215 11.729 462 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.26 % Allowed : 21.72 % 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 (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: -1.86 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6624.09 seconds wall clock time: 112 minutes 35.08 seconds (6755.08 seconds total)