Starting phenix.real_space_refine on Wed Sep 17 20:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh6_50441/09_2025/9fh6_50441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh6_50441/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fh6_50441/09_2025/9fh6_50441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh6_50441/09_2025/9fh6_50441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh6_50441/09_2025/9fh6_50441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh6_50441/09_2025/9fh6_50441.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.20 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: 1.13 Conformation dependent library (CDL) restraints added in 307.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 2.55 Time building geometry restraints manager: 1.55 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: 1.290 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG J 349 TYR 0.033 0.009 TYR J 310 PHE 0.027 0.008 PHE F 346 HIS 0.011 0.003 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01114 ( 5660) covalent geometry : angle 2.01311 ( 7580) hydrogen bonds : bond 0.05509 ( 98) hydrogen bonds : angle 6.30970 ( 294) *********************** 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 : 0.271 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: 0.3321 time to fit residues: 49.3353 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 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: 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 = 0.4450 r_free = 0.4450 target = 0.132936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.112749 restraints weight = 21288.966| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.57 r_work: 0.4113 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3995 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5660 Z= 0.201 Angle : 0.710 5.644 7580 Z= 0.389 Chirality : 0.053 0.127 860 Planarity : 0.004 0.028 960 Dihedral : 8.213 22.000 740 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.09 % Allowed : 12.66 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 349 TYR 0.016 0.004 TYR F 310 PHE 0.006 0.001 PHE F 378 HIS 0.008 0.002 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5660) covalent geometry : angle 0.71013 ( 7580) hydrogen bonds : bond 0.03153 ( 98) hydrogen bonds : angle 4.54284 ( 294) *********************** 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 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8029 (mttt) cc_final: 0.7703 (ttmt) REVERT: B 347 LYS cc_start: 0.8099 (mttt) cc_final: 0.7729 (ttmt) REVERT: C 347 LYS cc_start: 0.7817 (mttt) cc_final: 0.7435 (ttmt) REVERT: D 347 LYS cc_start: 0.7873 (mttt) cc_final: 0.7487 (ttmt) REVERT: D 349 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.6939 (mtp180) REVERT: E 347 LYS cc_start: 0.7781 (mttt) cc_final: 0.7372 (ttmt) REVERT: F 347 LYS cc_start: 0.7749 (mttt) cc_final: 0.7282 (ttmt) REVERT: G 347 LYS cc_start: 0.7901 (mttt) cc_final: 0.7487 (ttmt) REVERT: G 349 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7578 (mtp180) REVERT: H 347 LYS cc_start: 0.7857 (mttt) cc_final: 0.7470 (ttmt) REVERT: I 347 LYS cc_start: 0.8078 (mttt) cc_final: 0.7690 (ttmt) REVERT: J 347 LYS cc_start: 0.8079 (mttt) cc_final: 0.7671 (ttmt) outliers start: 7 outliers final: 7 residues processed: 102 average time/residue: 0.3786 time to fit residues: 44.5812 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 : 0.330 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.132380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.112898 restraints weight = 21221.163| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.59 r_work: 0.4132 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4013 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.129 Angle : 0.598 5.645 7580 Z= 0.317 Chirality : 0.050 0.123 860 Planarity : 0.003 0.028 960 Dihedral : 7.040 17.959 740 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.94 % Allowed : 15.16 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.010 0.002 TYR H 310 PHE 0.003 0.001 PHE F 378 HIS 0.007 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5660) covalent geometry : angle 0.59776 ( 7580) hydrogen bonds : bond 0.02458 ( 98) hydrogen bonds : angle 4.19101 ( 294) *********************** 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 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.335 Fit side-chains REVERT: A 347 LYS cc_start: 0.7888 (mttt) cc_final: 0.7570 (ttmt) REVERT: A 349 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7304 (mtp180) REVERT: B 347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7723 (ttmt) REVERT: C 349 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7022 (mtp180) REVERT: D 349 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.6877 (mtp180) REVERT: E 349 ARG cc_start: 0.7593 (mtp180) cc_final: 0.7387 (mtp180) REVERT: E 378 PHE cc_start: 0.6502 (t80) cc_final: 0.5948 (t80) REVERT: G 378 PHE cc_start: 0.6522 (t80) cc_final: 0.6186 (t80) outliers start: 6 outliers final: 6 residues processed: 91 average time/residue: 0.3171 time to fit residues: 34.0382 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 J residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 25 optimal weight: 0.0470 chunk 28 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.130998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.111330 restraints weight = 21405.577| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.62 r_work: 0.4109 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5660 Z= 0.145 Angle : 0.558 5.214 7580 Z= 0.297 Chirality : 0.050 0.124 860 Planarity : 0.003 0.028 960 Dihedral : 6.639 16.168 740 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.41 % Allowed : 15.78 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.010 0.002 TYR E 310 PHE 0.003 0.001 PHE I 346 HIS 0.006 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5660) covalent geometry : angle 0.55780 ( 7580) hydrogen bonds : bond 0.02233 ( 98) hydrogen bonds : angle 4.09764 ( 294) *********************** 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 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.277 Fit side-chains REVERT: A 349 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7321 (mtp180) REVERT: C 349 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7127 (mtp180) REVERT: D 349 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.6973 (mtp180) REVERT: E 349 ARG cc_start: 0.7593 (mtp180) cc_final: 0.7053 (mtp180) REVERT: E 378 PHE cc_start: 0.6353 (t80) cc_final: 0.5975 (t80) REVERT: G 378 PHE cc_start: 0.6612 (t80) cc_final: 0.6288 (t80) outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 0.3029 time to fit residues: 33.4550 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 : 0.287 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.109937 restraints weight = 21256.085| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.66 r_work: 0.4088 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5660 Z= 0.154 Angle : 0.550 4.946 7580 Z= 0.291 Chirality : 0.050 0.122 860 Planarity : 0.003 0.027 960 Dihedral : 6.458 15.983 740 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.09 % Allowed : 17.03 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.010 0.002 TYR H 310 PHE 0.003 0.001 PHE H 346 HIS 0.006 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5660) covalent geometry : angle 0.55020 ( 7580) hydrogen bonds : bond 0.02222 ( 98) hydrogen bonds : angle 4.05458 ( 294) *********************** 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 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.384 Fit side-chains REVERT: A 349 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7315 (mtp180) REVERT: B 342 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7025 (mp0) REVERT: B 349 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7271 (mtp180) REVERT: C 349 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.6982 (mtp180) REVERT: D 349 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.6877 (mtp180) REVERT: E 378 PHE cc_start: 0.6434 (t80) cc_final: 0.6123 (t80) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.2834 time to fit residues: 31.6619 Evaluate side-chains 82 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 J residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.127561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.107166 restraints weight = 21728.617| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.64 r_work: 0.4051 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.192 Angle : 0.566 4.761 7580 Z= 0.301 Chirality : 0.050 0.121 860 Planarity : 0.003 0.028 960 Dihedral : 6.532 16.345 740 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.25 % Allowed : 20.00 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.012 0.003 TYR F 310 PHE 0.006 0.001 PHE B 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5660) covalent geometry : angle 0.56576 ( 7580) hydrogen bonds : bond 0.02433 ( 98) hydrogen bonds : angle 4.05870 ( 294) *********************** 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 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.337 Fit side-chains REVERT: A 347 LYS cc_start: 0.7887 (mttt) cc_final: 0.7662 (ttmt) REVERT: B 347 LYS cc_start: 0.8073 (mttt) cc_final: 0.7697 (ttmt) REVERT: B 349 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7414 (mtp180) REVERT: C 349 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7164 (mtp180) REVERT: D 347 LYS cc_start: 0.7803 (mttt) cc_final: 0.7374 (ttmt) REVERT: D 349 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.6859 (mtp180) REVERT: G 347 LYS cc_start: 0.7894 (mttt) cc_final: 0.7471 (ttmt) REVERT: H 347 LYS cc_start: 0.7957 (mttt) cc_final: 0.7671 (ttmt) REVERT: H 378 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: J 347 LYS cc_start: 0.8228 (mttt) cc_final: 0.7743 (ttmt) outliers start: 8 outliers final: 7 residues processed: 103 average time/residue: 0.2732 time to fit residues: 33.2609 Evaluate side-chains 89 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 68 optimal weight: 0.0070 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.128631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.108595 restraints weight = 21609.690| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.64 r_work: 0.4075 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.138 Angle : 0.533 4.182 7580 Z= 0.280 Chirality : 0.049 0.123 860 Planarity : 0.003 0.030 960 Dihedral : 6.252 15.582 740 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.94 % Allowed : 22.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.008 0.002 TYR C 310 PHE 0.002 0.001 PHE D 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5660) covalent geometry : angle 0.53271 ( 7580) hydrogen bonds : bond 0.02052 ( 98) hydrogen bonds : angle 4.04428 ( 294) *********************** 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 88 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.371 Fit side-chains REVERT: A 349 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7457 (mtp180) REVERT: B 342 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7032 (mp0) REVERT: B 349 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7164 (mtp180) REVERT: C 349 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.6911 (mtp180) REVERT: D 349 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.6877 (mtp180) REVERT: F 340 LYS cc_start: 0.7799 (mttt) cc_final: 0.7525 (mttm) REVERT: G 347 LYS cc_start: 0.7861 (mttt) cc_final: 0.7445 (ttmt) REVERT: H 378 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.5910 (m-80) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.3002 time to fit residues: 31.3148 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 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 = 0.4389 r_free = 0.4389 target = 0.126948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.107082 restraints weight = 21704.350| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.54 r_work: 0.4049 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5660 Z= 0.185 Angle : 0.550 4.226 7580 Z= 0.293 Chirality : 0.050 0.122 860 Planarity : 0.003 0.029 960 Dihedral : 6.353 16.293 740 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.94 % Allowed : 23.12 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.012 0.003 TYR F 310 PHE 0.006 0.001 PHE D 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5660) covalent geometry : angle 0.55009 ( 7580) hydrogen bonds : bond 0.02321 ( 98) hydrogen bonds : angle 4.04111 ( 294) *********************** 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 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.319 Fit side-chains REVERT: A 347 LYS cc_start: 0.7934 (mttt) cc_final: 0.7710 (ttmt) REVERT: A 349 ARG cc_start: 0.8035 (ttp-110) cc_final: 0.7469 (mtp180) REVERT: B 342 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7031 (mp0) REVERT: B 347 LYS cc_start: 0.8110 (mttt) cc_final: 0.7832 (ttmt) REVERT: C 349 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.6941 (mtp180) REVERT: D 347 LYS cc_start: 0.7819 (mttt) cc_final: 0.7556 (ttmt) REVERT: D 349 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.6993 (mtp180) REVERT: E 347 LYS cc_start: 0.7703 (mttt) cc_final: 0.7474 (ttmt) REVERT: F 340 LYS cc_start: 0.7839 (mttt) cc_final: 0.7572 (mttm) REVERT: G 347 LYS cc_start: 0.7938 (mttt) cc_final: 0.7509 (ttmt) REVERT: H 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7589 (ttmt) REVERT: H 378 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6002 (m-80) REVERT: I 347 LYS cc_start: 0.8261 (mttt) cc_final: 0.7787 (ttmt) outliers start: 6 outliers final: 5 residues processed: 91 average time/residue: 0.3509 time to fit residues: 37.0023 Evaluate side-chains 87 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- 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 = 0.130645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.110764 restraints weight = 21124.077| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.56 r_work: 0.4117 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4663 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= 0.105 Angle : 0.514 4.191 7580 Z= 0.268 Chirality : 0.049 0.125 860 Planarity : 0.003 0.031 960 Dihedral : 5.953 15.008 740 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.94 % Allowed : 22.66 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.006 0.002 TYR G 310 PHE 0.001 0.000 PHE E 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5660) covalent geometry : angle 0.51386 ( 7580) hydrogen bonds : bond 0.01767 ( 98) hydrogen bonds : angle 4.02328 ( 294) *********************** 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 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.320 Fit side-chains REVERT: A 349 ARG cc_start: 0.7990 (ttp-110) cc_final: 0.7245 (mtp180) REVERT: B 349 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7170 (mtp180) REVERT: C 349 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.6863 (mtp180) REVERT: D 349 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.6853 (mtp180) REVERT: E 378 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: F 340 LYS cc_start: 0.7748 (mttt) cc_final: 0.7494 (mttm) REVERT: H 378 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5993 (m-80) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.3003 time to fit residues: 30.1867 Evaluate side-chains 82 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 341 SER Chi-restraints excluded: chain E residue 378 PHE 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 1 optimal weight: 0.0060 chunk 6 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.134523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.114642 restraints weight = 20924.195| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.60 r_work: 0.4169 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5660 Z= 0.087 Angle : 0.498 4.871 7580 Z= 0.258 Chirality : 0.049 0.124 860 Planarity : 0.003 0.033 960 Dihedral : 5.588 14.564 740 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.62 % Allowed : 23.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 349 TYR 0.005 0.002 TYR F 310 PHE 0.001 0.000 PHE D 346 HIS 0.006 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 5660) covalent geometry : angle 0.49772 ( 7580) hydrogen bonds : bond 0.01525 ( 98) hydrogen bonds : angle 3.96340 ( 294) ********************** 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: 4 poor density : 79 time to evaluate : 0.335 Fit side-chains REVERT: A 342 GLU cc_start: 0.8112 (tt0) cc_final: 0.7912 (mm-30) REVERT: A 349 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7461 (mtp180) REVERT: B 342 GLU cc_start: 0.8162 (mm-30) cc_final: 0.6987 (mp0) REVERT: B 349 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7148 (mtp180) REVERT: C 349 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.6856 (mtp85) REVERT: D 349 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.6794 (mtp180) REVERT: E 378 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: F 340 LYS cc_start: 0.7714 (mttt) cc_final: 0.7483 (mttm) REVERT: H 378 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5865 (m-80) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 0.3160 time to fit residues: 30.5433 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain E residue 378 PHE Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.114701 restraints weight = 21003.920| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.59 r_work: 0.4175 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 5660 Z= 0.200 Angle : 0.982 59.027 7580 Z= 0.615 Chirality : 0.050 0.329 860 Planarity : 0.003 0.044 960 Dihedral : 5.627 19.682 740 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.62 % Allowed : 23.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 349 TYR 0.006 0.002 TYR F 310 PHE 0.001 0.000 PHE J 346 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5660) covalent geometry : angle 0.98230 ( 7580) hydrogen bonds : bond 0.01544 ( 98) hydrogen bonds : angle 3.96372 ( 294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3162.07 seconds wall clock time: 54 minutes 30.45 seconds (3270.45 seconds total)