Starting phenix.real_space_refine on Wed Feb 12 02:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q2k_18111/02_2025/8q2k_18111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q2k_18111/02_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_18111/02_2025/8q2k_18111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q2k_18111/02_2025/8q2k_18111.map" model { file = "/net/cci-nas-00/data/ceres_data/8q2k_18111/02_2025/8q2k_18111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q2k_18111/02_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-5592/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: 4.48, per 1000 atoms: 0.64 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: 1.77 Conformation dependent library (CDL) restraints added in 683.7 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: 0.89 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: 2.49 Time building geometry restraints manager: 2.13 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: 3.540 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: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 : 0.609 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: 3.8332 time to fit residues: 483.8108 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 : 0.570 ------------------------------------------------------------------------------- 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 = 0.131265 restraints weight = 14550.915| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.38 r_work: 0.3819 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.558 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7702 (tt0) cc_final: 0.7277 (tp30) REVERT: A 369 LYS cc_start: 0.8259 (tttt) cc_final: 0.7953 (ttmp) REVERT: B 340 LYS cc_start: 0.8060 (tttt) cc_final: 0.7561 (tmtm) REVERT: B 342 GLU cc_start: 0.7669 (tt0) cc_final: 0.7464 (tt0) REVERT: C 338 GLU cc_start: 0.7719 (tt0) cc_final: 0.7337 (tp30) REVERT: C 349 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.5621 (mtt90) REVERT: C 351 GLN cc_start: 0.8568 (tt0) cc_final: 0.8259 (tt0) REVERT: D 340 LYS cc_start: 0.8432 (tttt) cc_final: 0.8003 (tptt) REVERT: D 349 ARG cc_start: 0.7268 (mtm180) cc_final: 0.5065 (pmt-80) REVERT: E 311 LYS cc_start: 0.7865 (mttt) cc_final: 0.6777 (mmtt) REVERT: E 338 GLU cc_start: 0.7663 (tt0) cc_final: 0.7231 (tp30) REVERT: E 369 LYS cc_start: 0.8381 (tttt) cc_final: 0.8034 (ttmp) REVERT: F 340 LYS cc_start: 0.7990 (tttt) cc_final: 0.7588 (tptt) REVERT: F 349 ARG cc_start: 0.6820 (mtm180) cc_final: 0.6005 (mmp80) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 3.8850 time to fit residues: 348.4030 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 : 0.648 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.140731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132158 restraints weight = 14869.103| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.38 r_work: 0.3838 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4434 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= 0.202 Angle : 0.500 4.426 4680 Z= 0.255 Chirality : 0.050 0.133 528 Planarity : 0.004 0.031 594 Dihedral : 4.858 12.330 462 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 16.41 % Favored : 82.58 % 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: -1.76 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.002 PHE A 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 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7711 (tt0) cc_final: 0.7321 (tp30) REVERT: A 351 GLN cc_start: 0.8441 (tt0) cc_final: 0.8110 (tt0) REVERT: B 340 LYS cc_start: 0.8040 (tttt) cc_final: 0.7616 (tmtm) REVERT: C 338 GLU cc_start: 0.7594 (tt0) cc_final: 0.7286 (tp30) REVERT: C 349 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.5649 (mtt90) REVERT: D 340 LYS cc_start: 0.8372 (tttt) cc_final: 0.8022 (tptt) REVERT: E 317 LYS cc_start: 0.8216 (mttt) cc_final: 0.7951 (ttmm) REVERT: E 338 GLU cc_start: 0.7624 (tt0) cc_final: 0.7270 (tp30) REVERT: F 340 LYS cc_start: 0.7978 (tttt) cc_final: 0.7652 (tptt) REVERT: F 349 ARG cc_start: 0.6943 (mtm180) cc_final: 0.6092 (mmp80) outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 3.6969 time to fit residues: 249.0623 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.145438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.137211 restraints weight = 14864.097| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.36 r_work: 0.3903 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4699 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 : 0.450 4.109 4680 Z= 0.225 Chirality : 0.051 0.125 528 Planarity : 0.003 0.022 594 Dihedral : 4.248 10.859 462 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 17.93 % 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: -1.45 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 374 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7692 (tt0) cc_final: 0.7304 (tp30) REVERT: A 351 GLN cc_start: 0.8391 (tt0) cc_final: 0.8157 (tt0) REVERT: B 340 LYS cc_start: 0.7950 (tttt) cc_final: 0.7592 (tmtm) REVERT: C 338 GLU cc_start: 0.7529 (tt0) cc_final: 0.7245 (tp30) REVERT: D 340 LYS cc_start: 0.8345 (tttt) cc_final: 0.8022 (tptt) REVERT: E 338 GLU cc_start: 0.7639 (tt0) cc_final: 0.7282 (tp30) REVERT: E 351 GLN cc_start: 0.8453 (tt0) cc_final: 0.8072 (tt0) REVERT: F 340 LYS cc_start: 0.7884 (tttt) cc_final: 0.7596 (tptt) REVERT: F 349 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6095 (mmp80) outliers start: 6 outliers final: 1 residues processed: 67 average time/residue: 3.0119 time to fit residues: 206.6669 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.140634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.132167 restraints weight = 14407.536| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.33 r_work: 0.3842 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4916 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= 0.235 Angle : 0.486 4.290 4680 Z= 0.246 Chirality : 0.050 0.127 528 Planarity : 0.003 0.023 594 Dihedral : 4.494 12.319 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.02 % Allowed : 18.18 % 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: -1.57 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.008 0.002 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 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 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7670 (tt0) cc_final: 0.7278 (tp30) REVERT: A 351 GLN cc_start: 0.8517 (tt0) cc_final: 0.8228 (tt0) REVERT: B 340 LYS cc_start: 0.8039 (tttt) cc_final: 0.7594 (tmtm) REVERT: C 338 GLU cc_start: 0.7615 (tt0) cc_final: 0.7321 (tp30) REVERT: C 349 ARG cc_start: 0.7008 (mtm-85) cc_final: 0.5772 (mtt90) REVERT: D 340 LYS cc_start: 0.8383 (tttt) cc_final: 0.7983 (tptt) REVERT: D 349 ARG cc_start: 0.7353 (mtm180) cc_final: 0.5021 (pmt-80) REVERT: E 338 GLU cc_start: 0.7653 (tt0) cc_final: 0.7306 (tp30) REVERT: E 351 GLN cc_start: 0.8471 (tt0) cc_final: 0.8126 (tt0) REVERT: F 340 LYS cc_start: 0.7966 (tttt) cc_final: 0.7593 (tptt) REVERT: F 349 ARG cc_start: 0.6993 (mtm180) cc_final: 0.6067 (mmp80) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 3.0621 time to fit residues: 207.1592 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131805 restraints weight = 14650.254| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.34 r_work: 0.3819 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5022 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= 0.225 Angle : 0.481 4.321 4680 Z= 0.243 Chirality : 0.050 0.122 528 Planarity : 0.003 0.024 594 Dihedral : 4.437 12.313 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.27 % Allowed : 18.43 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.007 0.001 PHE A 378 TYR 0.006 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 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7649 (tt0) cc_final: 0.7266 (tp30) REVERT: A 351 GLN cc_start: 0.8513 (tt0) cc_final: 0.8245 (tt0) REVERT: B 340 LYS cc_start: 0.8040 (tttt) cc_final: 0.7616 (tmtm) REVERT: C 338 GLU cc_start: 0.7613 (tt0) cc_final: 0.7319 (tp30) REVERT: C 349 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.5805 (mtt90) REVERT: D 340 LYS cc_start: 0.8404 (tttt) cc_final: 0.8008 (tptt) REVERT: D 349 ARG cc_start: 0.7364 (mtm180) cc_final: 0.5068 (pmt-80) REVERT: E 338 GLU cc_start: 0.7669 (tt0) cc_final: 0.7328 (tp30) REVERT: E 351 GLN cc_start: 0.8483 (tt0) cc_final: 0.8199 (tt0) REVERT: F 340 LYS cc_start: 0.7930 (tttt) cc_final: 0.7599 (tptt) REVERT: F 349 ARG cc_start: 0.7034 (mtm180) cc_final: 0.6054 (mmp80) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 3.0330 time to fit residues: 208.5106 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 359 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.141222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.132911 restraints weight = 14496.773| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.34 r_work: 0.3852 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.169 Angle : 0.457 4.171 4680 Z= 0.229 Chirality : 0.050 0.124 528 Planarity : 0.003 0.024 594 Dihedral : 4.203 11.807 462 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.85 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 (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: -1.68 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.005 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG B 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 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7647 (tt0) cc_final: 0.7446 (tt0) REVERT: A 351 GLN cc_start: 0.8478 (tt0) cc_final: 0.8236 (tt0) REVERT: B 340 LYS cc_start: 0.8037 (tttt) cc_final: 0.7608 (tmtm) REVERT: C 338 GLU cc_start: 0.7571 (tt0) cc_final: 0.7278 (tp30) REVERT: D 340 LYS cc_start: 0.8407 (tttt) cc_final: 0.8000 (tptt) REVERT: E 338 GLU cc_start: 0.7641 (tt0) cc_final: 0.7341 (tp30) REVERT: E 351 GLN cc_start: 0.8453 (tt0) cc_final: 0.8165 (tt0) REVERT: F 340 LYS cc_start: 0.7910 (tttt) cc_final: 0.7585 (tptt) REVERT: F 349 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6071 (mmp80) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 3.0108 time to fit residues: 188.2966 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.140870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132536 restraints weight = 14705.772| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.35 r_work: 0.3846 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.174 Angle : 0.459 4.171 4680 Z= 0.230 Chirality : 0.050 0.124 528 Planarity : 0.003 0.025 594 Dihedral : 4.161 11.567 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.52 % Allowed : 20.96 % 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: -1.73 (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 0.001 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 C 379 *********************** 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: 6 poor density : 57 time to evaluate : 0.623 Fit side-chains REVERT: A 338 GLU cc_start: 0.7654 (tt0) cc_final: 0.7276 (tp30) REVERT: A 351 GLN cc_start: 0.8454 (tt0) cc_final: 0.8233 (tt0) REVERT: B 340 LYS cc_start: 0.8046 (tttt) cc_final: 0.7622 (tmtm) REVERT: C 338 GLU cc_start: 0.7584 (tt0) cc_final: 0.7306 (tp30) REVERT: C 349 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.5834 (mtt90) REVERT: D 340 LYS cc_start: 0.8408 (tttt) cc_final: 0.8005 (tptt) REVERT: E 338 GLU cc_start: 0.7671 (tt0) cc_final: 0.7332 (tp30) REVERT: E 351 GLN cc_start: 0.8446 (tt0) cc_final: 0.8141 (tt0) REVERT: F 340 LYS cc_start: 0.7908 (tttt) cc_final: 0.7583 (tptt) REVERT: F 349 ARG cc_start: 0.7120 (mtm180) cc_final: 0.6086 (mmp80) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 2.9674 time to fit residues: 188.8716 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 : 0.525 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN D 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130131 restraints weight = 14751.179| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.35 r_work: 0.3804 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5283 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= 0.235 Angle : 0.476 4.287 4680 Z= 0.241 Chirality : 0.049 0.123 528 Planarity : 0.003 0.026 594 Dihedral : 4.319 11.912 462 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.02 % Allowed : 19.95 % Favored : 78.03 % 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 D 329 PHE 0.007 0.002 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG C 379 *********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.638 Fit side-chains REVERT: A 338 GLU cc_start: 0.7661 (tt0) cc_final: 0.7256 (tp30) REVERT: A 351 GLN cc_start: 0.8494 (tt0) cc_final: 0.8254 (tt0) REVERT: A 369 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8134 (ttmp) REVERT: B 340 LYS cc_start: 0.8058 (tttt) cc_final: 0.7634 (tmtm) REVERT: C 338 GLU cc_start: 0.7629 (tt0) cc_final: 0.7332 (tp30) REVERT: C 349 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.5897 (mtt90) REVERT: D 340 LYS cc_start: 0.8425 (tttt) cc_final: 0.8013 (tptt) REVERT: D 349 ARG cc_start: 0.7538 (mtm180) cc_final: 0.5120 (pmt-80) REVERT: E 338 GLU cc_start: 0.7674 (tt0) cc_final: 0.7321 (tp30) REVERT: E 351 GLN cc_start: 0.8451 (tt0) cc_final: 0.8184 (tt0) REVERT: F 340 LYS cc_start: 0.7918 (tttt) cc_final: 0.7567 (tptt) REVERT: F 349 ARG cc_start: 0.7135 (mtm180) cc_final: 0.6020 (mmp80) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 2.9959 time to fit residues: 193.6795 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 369 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 359 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.135906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127788 restraints weight = 15389.724| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.35 r_work: 0.3775 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.175 Angle : 0.457 4.177 4680 Z= 0.229 Chirality : 0.050 0.122 528 Planarity : 0.003 0.025 594 Dihedral : 4.152 11.529 462 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 20.96 % Favored : 78.03 % 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: -1.80 (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 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE B 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.640 Fit side-chains REVERT: A 338 GLU cc_start: 0.7695 (tt0) cc_final: 0.7301 (tp30) REVERT: A 351 GLN cc_start: 0.8453 (tt0) cc_final: 0.8234 (tt0) REVERT: B 340 LYS cc_start: 0.8031 (tttt) cc_final: 0.7622 (tmtm) REVERT: C 338 GLU cc_start: 0.7593 (tt0) cc_final: 0.7302 (tp30) REVERT: C 349 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6010 (mtt90) REVERT: D 340 LYS cc_start: 0.8405 (tttt) cc_final: 0.7996 (tptt) REVERT: E 338 GLU cc_start: 0.7633 (tt0) cc_final: 0.7282 (tp30) REVERT: E 351 GLN cc_start: 0.8452 (tt0) cc_final: 0.8151 (tt0) REVERT: F 340 LYS cc_start: 0.7899 (tttt) cc_final: 0.7540 (tptt) REVERT: F 349 ARG cc_start: 0.7196 (mtm180) cc_final: 0.6068 (mmp80) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 2.8696 time to fit residues: 171.1149 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU 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: 5.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128453 restraints weight = 15190.002| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.35 r_work: 0.3816 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.130 Angle : 0.438 4.046 4680 Z= 0.217 Chirality : 0.050 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 3.906 10.827 462 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.26 % Allowed : 20.96 % Favored : 77.78 % 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: -1.67 (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 HIS 0.001 0.000 HIS A 330 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6442.44 seconds wall clock time: 113 minutes 31.02 seconds (6811.02 seconds total)