Starting phenix.real_space_refine on Tue Jul 29 07:22:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh6_50441/07_2025/9fh6_50441.cif" } resolution = 3.3 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= 0.001 sd= 0.008 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 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.96, per 1000 atoms: 0.52 Number of scatterers: 11370 At special positions: 0 Unit cell: (146.248, 75.144, 45.248, 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 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5800 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: 2.92 Conformation dependent library (CDL) restraints added in 731.4 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.548A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU E 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.599A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 377 removed outlier: 6.686A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR E 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 318 Processing sheet with id=AB4, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB5, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.496A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL H 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LYS J 340 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.530A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU F 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU H 344 " --> pdb=" O ASP J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.584A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 377 removed outlier: 6.687A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 294 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: 3.74 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5790 1.13 - 1.30: 930 1.30 - 1.47: 1880 1.47 - 1.64: 2850 1.64 - 1.81: 10 Bond restraints: 11460 Sorted by residual: bond pdb=" CE1 PHE F 378 " pdb=" HE1 PHE F 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N THR J 319 " pdb=" H THR J 319 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN B 307 " pdb="HE22 GLN B 307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG D 349 " pdb="HH11 ARG D 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN A 327 " pdb="HD21 ASN A 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 11455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 17153 2.50 - 5.00: 2881 5.00 - 7.49: 805 7.49 - 9.99: 61 9.99 - 12.49: 10 Bond angle restraints: 20910 Sorted by residual: angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP D 345 " pdb=" CB ASP D 345 " pdb=" CG ASP D 345 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA ASP F 345 " pdb=" CB ASP F 345 " pdb=" CG ASP F 345 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" CA ASP E 345 " pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP C 345 " pdb=" CB ASP C 345 " pdb=" CG ASP C 345 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 ... (remaining 20905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 4368 11.99 - 23.98: 579 23.98 - 35.97: 173 35.97 - 47.96: 53 47.96 - 59.95: 97 Dihedral angle restraints: 5270 sinusoidal: 3000 harmonic: 2270 Sorted by residual: dihedral pdb=" CA VAL G 318 " pdb=" C VAL G 318 " pdb=" N THR G 319 " pdb=" CA THR G 319 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE C 346 " pdb=" C PHE C 346 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE F 346 " pdb=" C PHE F 346 " pdb=" N LYS F 347 " pdb=" CA LYS F 347 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 419 0.070 - 0.141: 336 0.141 - 0.211: 58 0.211 - 0.281: 39 0.281 - 0.351: 8 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA LYS J 311 " pdb=" N LYS J 311 " pdb=" C LYS J 311 " pdb=" CB LYS J 311 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LYS I 311 " pdb=" N LYS I 311 " pdb=" C LYS I 311 " pdb=" CB LYS I 311 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS I 347 " pdb=" N LYS I 347 " pdb=" C LYS I 347 " pdb=" CB LYS I 347 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 336 " -0.062 2.00e-02 2.50e+03 5.74e-02 4.94e+01 pdb=" CD GLN A 336 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 336 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN A 336 " 0.038 2.00e-02 2.50e+03 pdb="HE21 GLN A 336 " 0.054 2.00e-02 2.50e+03 pdb="HE22 GLN A 336 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 336 " -0.062 2.00e-02 2.50e+03 5.60e-02 4.71e+01 pdb=" CD GLN B 336 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN B 336 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 GLN B 336 " 0.045 2.00e-02 2.50e+03 pdb="HE21 GLN B 336 " 0.045 2.00e-02 2.50e+03 pdb="HE22 GLN B 336 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 336 " -0.058 2.00e-02 2.50e+03 5.36e-02 4.31e+01 pdb=" CD GLN F 336 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN F 336 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 GLN F 336 " 0.046 2.00e-02 2.50e+03 pdb="HE21 GLN F 336 " 0.041 2.00e-02 2.50e+03 pdb="HE22 GLN F 336 " -0.090 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1251 2.22 - 2.82: 21784 2.82 - 3.41: 30396 3.41 - 4.01: 41558 4.01 - 4.60: 59544 Nonbonded interactions: 154533 Sorted by model distance: nonbonded pdb=" HG SER A 356 " pdb=" OD1 ASP A 358 " model vdw 1.626 2.450 nonbonded pdb=" HG SER B 356 " pdb=" OD1 ASP B 358 " model vdw 1.626 2.450 nonbonded pdb=" HG SER G 356 " pdb=" OD1 ASP G 358 " model vdw 1.640 2.450 nonbonded pdb=" HG SER H 356 " pdb=" OD1 ASP H 358 " model vdw 1.640 2.450 nonbonded pdb=" HG SER F 356 " pdb=" OD1 ASP F 358 " model vdw 1.641 2.450 ... (remaining 154528 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.460 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.740 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 0.038 5660 Z= 0.710 Angle : 2.013 7.856 7580 Z= 1.320 Chirality : 0.101 0.351 860 Planarity : 0.011 0.034 960 Dihedral : 12.085 57.884 2160 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Cbeta Deviations : 0.31 % 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: -2.20 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS E 330 PHE 0.027 0.008 PHE F 346 TYR 0.033 0.009 TYR J 310 ARG 0.002 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 98) hydrogen bonds : angle 6.30970 ( 294) covalent geometry : bond 0.01114 ( 5660) covalent geometry : angle 2.01311 ( 7580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.6649 time to fit residues: 99.7193 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.130221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.110107 restraints weight = 21474.090| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.51 r_work: 0.4077 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 5660 Z= 0.263 Angle : 0.733 5.732 7580 Z= 0.402 Chirality : 0.053 0.132 860 Planarity : 0.005 0.028 960 Dihedral : 8.453 22.985 740 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.41 % Allowed : 12.97 % Favored : 85.62 % 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: -2.69 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 330 PHE 0.006 0.001 PHE F 378 TYR 0.017 0.004 TYR F 310 ARG 0.004 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 98) hydrogen bonds : angle 4.52206 ( 294) covalent geometry : bond 0.00602 ( 5660) covalent geometry : angle 0.73302 ( 7580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8072 (mttt) cc_final: 0.7740 (ttmt) REVERT: B 347 LYS cc_start: 0.8124 (mttt) cc_final: 0.7746 (ttmt) REVERT: C 347 LYS cc_start: 0.7881 (mttt) cc_final: 0.7507 (ttmt) REVERT: D 347 LYS cc_start: 0.7864 (mttt) cc_final: 0.7485 (ttmt) REVERT: D 349 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.6961 (mtp180) REVERT: E 347 LYS cc_start: 0.7800 (mttt) cc_final: 0.7415 (ttmt) REVERT: F 347 LYS cc_start: 0.7801 (mttt) cc_final: 0.7320 (ttmt) REVERT: G 347 LYS cc_start: 0.7922 (mttt) cc_final: 0.7519 (ttmt) REVERT: G 349 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7516 (mtp180) REVERT: H 347 LYS cc_start: 0.7955 (mttt) cc_final: 0.7555 (ttmt) REVERT: I 347 LYS cc_start: 0.8079 (mttt) cc_final: 0.7698 (ttmt) REVERT: J 347 LYS cc_start: 0.8126 (mttt) cc_final: 0.7733 (ttmt) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.7057 time to fit residues: 86.7484 Evaluate side-chains 87 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.134014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.114722 restraints weight = 20861.608| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.60 r_work: 0.4161 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5660 Z= 0.098 Angle : 0.579 5.694 7580 Z= 0.307 Chirality : 0.050 0.126 860 Planarity : 0.003 0.028 960 Dihedral : 7.020 17.592 740 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.72 % Allowed : 14.53 % Favored : 83.75 % 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: -2.65 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 330 PHE 0.003 0.001 PHE D 346 TYR 0.007 0.002 TYR E 310 ARG 0.001 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02319 ( 98) hydrogen bonds : angle 4.26523 ( 294) covalent geometry : bond 0.00218 ( 5660) covalent geometry : angle 0.57881 ( 7580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.907 Fit side-chains REVERT: A 349 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7245 (mtp180) REVERT: C 349 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.6908 (mtp180) REVERT: D 349 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.6843 (mtp180) REVERT: G 378 PHE cc_start: 0.6515 (t80) cc_final: 0.6201 (t80) outliers start: 11 outliers final: 11 residues processed: 96 average time/residue: 0.6147 time to fit residues: 70.3346 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.128390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.108517 restraints weight = 21490.801| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.60 r_work: 0.4073 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5660 Z= 0.179 Angle : 0.577 5.277 7580 Z= 0.310 Chirality : 0.050 0.121 860 Planarity : 0.003 0.028 960 Dihedral : 6.898 17.000 740 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.72 % Allowed : 16.25 % Favored : 82.03 % 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: -2.66 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 330 PHE 0.005 0.001 PHE G 346 TYR 0.013 0.003 TYR E 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02459 ( 98) hydrogen bonds : angle 4.12239 ( 294) covalent geometry : bond 0.00405 ( 5660) covalent geometry : angle 0.57651 ( 7580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.942 Fit side-chains REVERT: A 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7615 (ttmt) REVERT: A 349 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7322 (mtp180) REVERT: B 347 LYS cc_start: 0.8107 (mttt) cc_final: 0.7680 (ttmt) REVERT: C 349 ARG cc_start: 0.7787 (ttp-110) cc_final: 0.7012 (mtp180) REVERT: D 347 LYS cc_start: 0.7770 (mttt) cc_final: 0.7449 (ttmt) REVERT: D 349 ARG cc_start: 0.7688 (ttp-110) cc_final: 0.6939 (mtp180) REVERT: E 378 PHE cc_start: 0.6345 (t80) cc_final: 0.5920 (t80) REVERT: G 347 LYS cc_start: 0.7789 (mttt) cc_final: 0.7409 (ttmt) REVERT: G 378 PHE cc_start: 0.6624 (t80) cc_final: 0.6283 (t80) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.6065 time to fit residues: 69.7472 Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 0.0570 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.130241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.110528 restraints weight = 21236.161| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.59 r_work: 0.4103 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5660 Z= 0.141 Angle : 0.535 4.960 7580 Z= 0.285 Chirality : 0.049 0.125 860 Planarity : 0.003 0.028 960 Dihedral : 6.500 15.896 740 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.56 % Allowed : 17.19 % Favored : 81.25 % 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: -2.69 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 330 PHE 0.002 0.001 PHE J 346 TYR 0.009 0.002 TYR H 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02137 ( 98) hydrogen bonds : angle 4.10324 ( 294) covalent geometry : bond 0.00309 ( 5660) covalent geometry : angle 0.53461 ( 7580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.892 Fit side-chains REVERT: A 349 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7300 (mtp180) REVERT: B 342 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7053 (mp0) REVERT: C 349 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7132 (mtp180) REVERT: D 349 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.6900 (mtp180) REVERT: D 356 SER cc_start: 0.8810 (p) cc_final: 0.8599 (p) REVERT: E 378 PHE cc_start: 0.6432 (t80) cc_final: 0.6048 (t80) REVERT: G 378 PHE cc_start: 0.6639 (t80) cc_final: 0.6369 (t80) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.5954 time to fit residues: 66.7378 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.130776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.110854 restraints weight = 21266.451| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.60 r_work: 0.4106 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.129 Angle : 0.528 4.725 7580 Z= 0.277 Chirality : 0.049 0.122 860 Planarity : 0.003 0.029 960 Dihedral : 6.207 15.395 740 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.41 % Allowed : 18.12 % Favored : 80.47 % 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: -2.70 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 330 PHE 0.002 0.001 PHE J 346 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01986 ( 98) hydrogen bonds : angle 4.06313 ( 294) covalent geometry : bond 0.00282 ( 5660) covalent geometry : angle 0.52765 ( 7580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.154 Fit side-chains REVERT: A 349 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7303 (mtp180) REVERT: B 342 GLU cc_start: 0.8222 (mm-30) cc_final: 0.6988 (mp0) REVERT: B 349 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7352 (mtp180) REVERT: C 349 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7034 (mtp180) REVERT: D 349 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.6771 (mtp180) REVERT: E 378 PHE cc_start: 0.6297 (t80) cc_final: 0.6048 (t80) REVERT: H 378 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.5784 (m-80) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.7419 time to fit residues: 89.1874 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.129490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.109227 restraints weight = 21615.351| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.65 r_work: 0.4081 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.146 Angle : 0.528 4.593 7580 Z= 0.279 Chirality : 0.049 0.120 860 Planarity : 0.003 0.029 960 Dihedral : 6.169 15.524 740 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.09 % Allowed : 19.69 % Favored : 79.22 % 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: -2.74 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 330 PHE 0.004 0.001 PHE D 346 TYR 0.009 0.002 TYR E 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02058 ( 98) hydrogen bonds : angle 4.06436 ( 294) covalent geometry : bond 0.00320 ( 5660) covalent geometry : angle 0.52822 ( 7580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.990 Fit side-chains REVERT: A 349 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7324 (mtp180) REVERT: B 342 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7027 (mp0) REVERT: B 349 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7374 (mtp180) REVERT: C 349 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7141 (mtp180) REVERT: D 349 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.6875 (mtp180) REVERT: F 340 LYS cc_start: 0.7800 (mttt) cc_final: 0.7521 (mttm) REVERT: H 378 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.5859 (m-80) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.6549 time to fit residues: 71.8147 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 378 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.130564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.110549 restraints weight = 21404.736| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.58 r_work: 0.4108 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5660 Z= 0.127 Angle : 0.515 5.040 7580 Z= 0.271 Chirality : 0.049 0.121 860 Planarity : 0.003 0.029 960 Dihedral : 6.008 15.080 740 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.09 % Allowed : 20.94 % Favored : 77.97 % 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: -2.67 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 330 PHE 0.002 0.001 PHE E 378 TYR 0.008 0.002 TYR C 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01885 ( 98) hydrogen bonds : angle 4.04621 ( 294) covalent geometry : bond 0.00279 ( 5660) covalent geometry : angle 0.51546 ( 7580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.013 Fit side-chains REVERT: A 349 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7459 (mtp180) REVERT: B 342 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7001 (mp0) REVERT: B 349 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7147 (mtp180) REVERT: C 349 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7071 (mtp180) REVERT: D 349 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.6843 (mtp180) REVERT: F 340 LYS cc_start: 0.7722 (mttt) cc_final: 0.7464 (mttm) REVERT: H 378 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.5904 (m-80) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.6128 time to fit residues: 63.7339 Evaluate side-chains 81 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 378 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.127981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.107595 restraints weight = 21742.653| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.61 r_work: 0.4060 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5660 Z= 0.181 Angle : 0.542 5.034 7580 Z= 0.288 Chirality : 0.050 0.120 860 Planarity : 0.003 0.028 960 Dihedral : 6.197 15.781 740 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.09 % Allowed : 22.03 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.71 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 330 PHE 0.007 0.001 PHE D 346 TYR 0.011 0.003 TYR F 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02238 ( 98) hydrogen bonds : angle 4.06715 ( 294) covalent geometry : bond 0.00398 ( 5660) covalent geometry : angle 0.54201 ( 7580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.990 Fit side-chains REVERT: A 347 LYS cc_start: 0.7899 (mttt) cc_final: 0.7684 (ttmt) REVERT: A 349 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7485 (mtp180) REVERT: B 342 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7010 (mp0) REVERT: B 347 LYS cc_start: 0.8070 (mttt) cc_final: 0.7811 (ttmt) REVERT: B 349 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7195 (mtp180) REVERT: C 349 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.6883 (mtp85) REVERT: D 349 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.6921 (mtp180) REVERT: F 340 LYS cc_start: 0.7754 (mttt) cc_final: 0.7493 (mttm) REVERT: G 347 LYS cc_start: 0.7924 (mttt) cc_final: 0.7486 (ttmt) REVERT: H 378 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5971 (m-80) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.6316 time to fit residues: 68.4810 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.130367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.110126 restraints weight = 21328.348| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.60 r_work: 0.4098 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5660 Z= 0.116 Angle : 0.511 4.804 7580 Z= 0.268 Chirality : 0.049 0.120 860 Planarity : 0.003 0.030 960 Dihedral : 5.915 15.127 740 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.25 % Allowed : 22.66 % Favored : 76.09 % 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: -2.61 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 330 PHE 0.001 0.000 PHE J 346 TYR 0.007 0.002 TYR E 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.01795 ( 98) hydrogen bonds : angle 4.03881 ( 294) covalent geometry : bond 0.00254 ( 5660) covalent geometry : angle 0.51092 ( 7580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.909 Fit side-chains REVERT: A 349 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7473 (mtp180) REVERT: B 349 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7185 (mtp180) REVERT: C 349 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.6883 (mtp180) REVERT: D 349 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.6799 (mtp180) REVERT: F 340 LYS cc_start: 0.7758 (mttt) cc_final: 0.7507 (mttm) REVERT: H 378 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.5994 (m-80) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.6378 time to fit residues: 62.8043 Evaluate side-chains 80 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain H residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.107217 restraints weight = 21673.134| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.59 r_work: 0.4047 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5660 Z= 0.183 Angle : 0.539 4.931 7580 Z= 0.287 Chirality : 0.050 0.121 860 Planarity : 0.003 0.030 960 Dihedral : 6.131 15.736 740 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.94 % Allowed : 22.81 % Favored : 76.25 % 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: -2.71 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 330 PHE 0.006 0.001 PHE D 346 TYR 0.011 0.003 TYR F 310 ARG 0.003 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02228 ( 98) hydrogen bonds : angle 4.05316 ( 294) covalent geometry : bond 0.00401 ( 5660) covalent geometry : angle 0.53894 ( 7580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.16 seconds wall clock time: 115 minutes 12.91 seconds (6912.91 seconds total)