Starting phenix.real_space_refine on Fri Aug 22 18:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.map" model { file = "/net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cgx_45588/08_2025/9cgx_45588.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2142 2.51 5 N 630 2.21 5 O 642 1.98 5 H 3540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 6960 At special positions: 0 Unit cell: (149.46, 76.32, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 630 7.00 C 2142 6.00 H 3540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 280.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.762A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) 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 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.649A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.844A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.444A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.680A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'B' and resid 317 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: 6.545A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.325A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.819A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AC1, first strand: chain 'B' and resid 369 through 371 Processing sheet with id=AC2, first strand: chain 'B' and resid 369 through 371 90 hydrogen bonds defined for protein. 267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3534 1.12 - 1.29: 576 1.29 - 1.47: 1061 1.47 - 1.64: 1837 1.64 - 1.81: 6 Bond restraints: 7014 Sorted by residual: bond pdb=" N VAL B 363 " pdb=" H VAL B 363 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL B 339 " pdb=" H VAL B 339 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LYS D 347 " pdb=" H LYS D 347 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N SER E 324 " pdb=" H SER E 324 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 7009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 10618 2.54 - 5.07: 1645 5.07 - 7.61: 487 7.61 - 10.14: 24 10.14 - 12.68: 6 Bond angle restraints: 12780 Sorted by residual: angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" CA ASP B 345 " pdb=" CB ASP B 345 " pdb=" CG ASP B 345 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" CA ASP C 345 " pdb=" CB ASP C 345 " pdb=" CG ASP C 345 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.30e+01 ... (remaining 12775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 2851 17.63 - 35.25: 204 35.25 - 52.88: 85 52.88 - 70.50: 84 70.50 - 88.13: 4 Dihedral angle restraints: 3228 sinusoidal: 1848 harmonic: 1380 Sorted by residual: dihedral pdb=" CA LEU B 325 " pdb=" C LEU B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU E 325 " pdb=" C LEU E 325 " pdb=" N GLY E 326 " pdb=" CA GLY E 326 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU D 325 " pdb=" C LEU D 325 " pdb=" N GLY D 326 " pdb=" CA GLY D 326 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 3225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 230 0.056 - 0.113: 169 0.113 - 0.169: 73 0.169 - 0.225: 34 0.225 - 0.282: 10 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG C 379 " pdb=" N ARG C 379 " pdb=" C ARG C 379 " pdb=" CB ARG C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ARG D 379 " pdb=" N ARG D 379 " pdb=" C ARG D 379 " pdb=" CB ARG D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 513 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.168 2.00e-02 2.50e+03 1.18e-01 4.15e+02 pdb=" CG PHE E 346 " 0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.147 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " -0.134 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.107 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " 0.083 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " -0.208 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " -0.101 2.00e-02 2.50e+03 5.35e-02 8.57e+01 pdb=" CG PHE B 346 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " 0.107 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.106 2.00e-02 2.50e+03 5.93e-02 7.91e+01 pdb=" CG HIS D 330 " 0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.047 2.00e-02 2.50e+03 pdb=" HE2 HIS D 330 " -0.077 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 517 2.17 - 2.77: 11836 2.77 - 3.38: 18315 3.38 - 3.99: 24527 3.99 - 4.60: 34690 Nonbonded interactions: 89885 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.605 2.450 ... (remaining 89880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 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 0.037 3474 Z= 0.692 Angle : 2.027 12.677 4644 Z= 1.311 Chirality : 0.094 0.282 516 Planarity : 0.012 0.098 594 Dihedral : 13.192 88.128 1344 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 2.78 % Allowed : 4.86 % Favored : 92.36 % Rotamer: Outliers : 2.82 % Allowed : 3.08 % Favored : 94.10 % 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 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG F 349 TYR 0.060 0.020 TYR E 310 PHE 0.164 0.019 PHE E 346 HIS 0.016 0.004 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.01082 ( 3474) covalent geometry : angle 2.02662 ( 4644) hydrogen bonds : bond 0.13631 ( 88) hydrogen bonds : angle 8.00024 ( 267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.201 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 REVERT: A 311 LYS cc_start: 0.8129 (tttt) cc_final: 0.7598 (ttmm) REVERT: A 331 LYS cc_start: 0.8052 (mttt) cc_final: 0.7850 (mtmm) REVERT: A 338 GLU cc_start: 0.7369 (tt0) cc_final: 0.6878 (mm-30) REVERT: A 342 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6873 (mp0) REVERT: A 369 LYS cc_start: 0.7903 (mttt) cc_final: 0.7614 (mmtp) REVERT: B 321 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7873 (mtpt) REVERT: B 338 GLU cc_start: 0.7849 (tt0) cc_final: 0.7407 (mp0) REVERT: B 342 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6528 (mp0) REVERT: B 343 LYS cc_start: 0.7793 (mptt) cc_final: 0.7509 (mppt) REVERT: B 348 ASP cc_start: 0.7879 (t0) cc_final: 0.7654 (t0) REVERT: B 351 GLN cc_start: 0.7893 (mt0) cc_final: 0.7692 (mt0) REVERT: B 373 THR cc_start: 0.7127 (m) cc_final: 0.6817 (p) REVERT: B 379 ARG cc_start: 0.6423 (ttt180) cc_final: 0.5833 (ttp-110) REVERT: C 315 LEU cc_start: 0.8292 (mt) cc_final: 0.8069 (mm) REVERT: C 321 LYS cc_start: 0.7320 (mtmt) cc_final: 0.7071 (mtpt) REVERT: C 331 LYS cc_start: 0.7781 (mttt) cc_final: 0.7329 (mtpp) REVERT: C 338 GLU cc_start: 0.7060 (tt0) cc_final: 0.6803 (tt0) REVERT: C 340 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7026 (tptp) REVERT: C 345 ASP cc_start: 0.7836 (m-30) cc_final: 0.7597 (m-30) REVERT: C 349 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6504 (mtp85) REVERT: C 369 LYS cc_start: 0.7169 (mttt) cc_final: 0.6522 (mtpt) REVERT: D 315 LEU cc_start: 0.8368 (mt) cc_final: 0.7936 (mm) REVERT: D 317 LYS cc_start: 0.6758 (mttp) cc_final: 0.6283 (ttmt) REVERT: D 321 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6203 (tmtt) REVERT: E 311 LYS cc_start: 0.7346 (tttt) cc_final: 0.6449 (tppt) REVERT: E 317 LYS cc_start: 0.6759 (mttt) cc_final: 0.6461 (ttpt) REVERT: E 321 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6021 (mmtm) REVERT: E 327 ASN cc_start: 0.7408 (t0) cc_final: 0.7195 (t0) REVERT: E 343 LYS cc_start: 0.7732 (mttt) cc_final: 0.6381 (mmpt) REVERT: E 353 LYS cc_start: 0.7912 (tttt) cc_final: 0.7571 (tttm) REVERT: E 370 LYS cc_start: 0.7962 (tttt) cc_final: 0.5912 (mttt) REVERT: F 311 LYS cc_start: 0.7423 (tttt) cc_final: 0.6567 (tppt) REVERT: F 327 ASN cc_start: 0.7434 (m-40) cc_final: 0.7181 (m-40) REVERT: F 338 GLU cc_start: 0.7201 (tt0) cc_final: 0.6427 (mp0) REVERT: F 343 LYS cc_start: 0.7277 (mptt) cc_final: 0.6460 (mmtm) REVERT: F 358 ASP cc_start: 0.7483 (m-30) cc_final: 0.7214 (m-30) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 1.5305 time to fit residues: 215.7112 Evaluate side-chains 102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.154178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.128465 restraints weight = 11160.238| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.02 r_work: 0.3936 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3474 Z= 0.164 Angle : 0.771 7.017 4644 Z= 0.391 Chirality : 0.054 0.139 516 Planarity : 0.003 0.023 594 Dihedral : 8.010 24.667 459 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.41 % Favored : 92.36 % Rotamer: Outliers : 1.28 % Allowed : 12.05 % Favored : 86.67 % 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: -2.35 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.013 0.003 TYR C 310 PHE 0.017 0.002 PHE E 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3474) covalent geometry : angle 0.77130 ( 4644) hydrogen bonds : bond 0.03232 ( 88) hydrogen bonds : angle 5.59920 ( 267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8118 (tt0) cc_final: 0.7597 (mp0) REVERT: A 342 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7347 (mp0) REVERT: A 351 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: A 379 ARG cc_start: 0.6003 (ttt180) cc_final: 0.4877 (ttp80) REVERT: B 338 GLU cc_start: 0.8374 (tt0) cc_final: 0.7866 (mp0) REVERT: B 342 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6979 (mp0) REVERT: B 343 LYS cc_start: 0.7965 (mptt) cc_final: 0.7579 (mppt) REVERT: B 348 ASP cc_start: 0.8066 (t0) cc_final: 0.7652 (t0) REVERT: B 351 GLN cc_start: 0.8271 (mt0) cc_final: 0.8030 (mt0) REVERT: B 379 ARG cc_start: 0.6549 (ttt180) cc_final: 0.5607 (ttp-110) REVERT: C 338 GLU cc_start: 0.8170 (tt0) cc_final: 0.7663 (tm-30) REVERT: C 340 LYS cc_start: 0.8579 (mtmt) cc_final: 0.7886 (tptp) REVERT: C 349 ARG cc_start: 0.7525 (mtm180) cc_final: 0.6920 (mtp85) REVERT: D 317 LYS cc_start: 0.7543 (mttp) cc_final: 0.7088 (ptmt) REVERT: D 321 LYS cc_start: 0.7876 (ttmt) cc_final: 0.6991 (tmmt) REVERT: D 342 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6951 (mt-10) REVERT: E 311 LYS cc_start: 0.7424 (tttt) cc_final: 0.6545 (tppt) REVERT: E 317 LYS cc_start: 0.7197 (mttt) cc_final: 0.6983 (ptmt) REVERT: F 311 LYS cc_start: 0.7698 (tttt) cc_final: 0.6718 (tppt) REVERT: F 343 LYS cc_start: 0.7562 (mptt) cc_final: 0.7197 (mppt) outliers start: 5 outliers final: 2 residues processed: 103 average time/residue: 1.3541 time to fit residues: 142.6501 Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.152134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.126504 restraints weight = 11151.711| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.96 r_work: 0.3914 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3474 Z= 0.133 Angle : 0.612 4.345 4644 Z= 0.313 Chirality : 0.051 0.133 516 Planarity : 0.003 0.023 594 Dihedral : 7.150 20.921 456 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.82 % Rotamer: Outliers : 1.54 % Allowed : 17.44 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.34 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.011 0.002 TYR C 310 PHE 0.013 0.002 PHE E 346 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3474) covalent geometry : angle 0.61196 ( 4644) hydrogen bonds : bond 0.02465 ( 88) hydrogen bonds : angle 4.90590 ( 267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7206 (mp0) REVERT: A 351 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: A 369 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7657 (mttm) REVERT: A 379 ARG cc_start: 0.5960 (ttt180) cc_final: 0.3483 (mmp-170) REVERT: B 342 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6983 (mp0) REVERT: B 343 LYS cc_start: 0.8048 (mptt) cc_final: 0.7670 (mppt) REVERT: B 351 GLN cc_start: 0.8183 (mt0) cc_final: 0.7963 (mt0) REVERT: B 379 ARG cc_start: 0.6283 (ttt180) cc_final: 0.5412 (ttp-110) REVERT: C 349 ARG cc_start: 0.7689 (mtm180) cc_final: 0.7072 (mtp85) REVERT: D 317 LYS cc_start: 0.7518 (mttp) cc_final: 0.7026 (ptmt) REVERT: E 311 LYS cc_start: 0.7543 (tttt) cc_final: 0.6562 (tppt) REVERT: E 376 LEU cc_start: 0.8179 (tp) cc_final: 0.7967 (tm) REVERT: F 311 LYS cc_start: 0.7763 (tttt) cc_final: 0.6956 (tppt) REVERT: F 343 LYS cc_start: 0.7793 (mptt) cc_final: 0.7373 (mppt) outliers start: 6 outliers final: 1 residues processed: 81 average time/residue: 1.4385 time to fit residues: 119.1430 Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.150558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.124521 restraints weight = 11176.161| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.95 r_work: 0.3879 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3474 Z= 0.141 Angle : 0.583 4.429 4644 Z= 0.296 Chirality : 0.051 0.132 516 Planarity : 0.003 0.025 594 Dihedral : 6.838 20.066 456 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 2.05 % Allowed : 17.95 % Favored : 80.00 % 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: -2.48 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.010 0.002 TYR D 310 PHE 0.010 0.002 PHE D 346 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3474) covalent geometry : angle 0.58336 ( 4644) hydrogen bonds : bond 0.02171 ( 88) hydrogen bonds : angle 4.64766 ( 267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7128 (mp0) REVERT: A 349 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7340 (mtm180) REVERT: A 369 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7799 (mttm) REVERT: A 379 ARG cc_start: 0.5956 (ttt180) cc_final: 0.3542 (mmp-170) REVERT: B 331 LYS cc_start: 0.8895 (mttt) cc_final: 0.8640 (mtpt) REVERT: B 340 LYS cc_start: 0.8547 (mttt) cc_final: 0.8286 (mttt) REVERT: B 342 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7069 (mp0) REVERT: B 343 LYS cc_start: 0.8042 (mptt) cc_final: 0.7634 (mppt) REVERT: B 351 GLN cc_start: 0.8270 (mt0) cc_final: 0.8040 (mt0) REVERT: B 379 ARG cc_start: 0.6359 (ttt180) cc_final: 0.5399 (mpp80) REVERT: C 340 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8243 (ttmm) REVERT: C 342 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 349 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7342 (mtp180) REVERT: D 317 LYS cc_start: 0.7519 (mttp) cc_final: 0.7013 (ptmt) REVERT: D 342 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6984 (mt-10) REVERT: E 311 LYS cc_start: 0.7560 (tttt) cc_final: 0.6690 (tptt) REVERT: E 314 ASP cc_start: 0.8179 (t0) cc_final: 0.7924 (t0) REVERT: F 343 LYS cc_start: 0.7991 (mptt) cc_final: 0.7534 (mppt) REVERT: F 370 LYS cc_start: 0.8347 (tttt) cc_final: 0.6709 (mttt) outliers start: 8 outliers final: 1 residues processed: 85 average time/residue: 1.5834 time to fit residues: 137.5098 Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.150234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124006 restraints weight = 11191.306| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.96 r_work: 0.3878 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3474 Z= 0.134 Angle : 0.556 4.096 4644 Z= 0.283 Chirality : 0.051 0.136 516 Planarity : 0.003 0.026 594 Dihedral : 6.653 18.790 456 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.51 % 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 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.011 0.002 TYR E 310 PHE 0.007 0.001 PHE F 378 HIS 0.001 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3474) covalent geometry : angle 0.55600 ( 4644) hydrogen bonds : bond 0.02073 ( 88) hydrogen bonds : angle 4.49418 ( 267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8480 (mttm) REVERT: A 342 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7144 (mp0) REVERT: A 351 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: A 379 ARG cc_start: 0.6170 (ttt180) cc_final: 0.3711 (mmp-170) REVERT: B 331 LYS cc_start: 0.8893 (mttt) cc_final: 0.8640 (mtpt) REVERT: B 340 LYS cc_start: 0.8471 (mttt) cc_final: 0.8210 (mttt) REVERT: B 342 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7090 (mp0) REVERT: B 343 LYS cc_start: 0.8089 (mptt) cc_final: 0.7650 (mppt) REVERT: B 351 GLN cc_start: 0.8314 (mt0) cc_final: 0.8077 (mt0) REVERT: B 379 ARG cc_start: 0.6573 (ttt180) cc_final: 0.5468 (mpp80) REVERT: C 340 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8041 (ttmm) REVERT: C 342 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: C 349 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7314 (mtp180) REVERT: D 317 LYS cc_start: 0.7579 (mttp) cc_final: 0.6995 (ttmt) REVERT: D 342 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6985 (mt-10) REVERT: E 314 ASP cc_start: 0.8160 (t0) cc_final: 0.7843 (t0) REVERT: F 311 LYS cc_start: 0.8429 (tttp) cc_final: 0.7337 (tppt) REVERT: F 321 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7837 (mttp) REVERT: F 343 LYS cc_start: 0.7990 (mptt) cc_final: 0.7621 (mppt) outliers start: 10 outliers final: 2 residues processed: 76 average time/residue: 1.4358 time to fit residues: 111.7575 Evaluate side-chains 73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.150231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.124216 restraints weight = 11273.227| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.95 r_work: 0.3871 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3474 Z= 0.131 Angle : 0.546 4.998 4644 Z= 0.279 Chirality : 0.051 0.137 516 Planarity : 0.003 0.028 594 Dihedral : 6.536 18.778 456 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.67 % Rotamer: Outliers : 1.54 % Allowed : 18.46 % Favored : 80.00 % 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: -2.61 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.009 0.002 TYR C 310 PHE 0.006 0.001 PHE D 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3474) covalent geometry : angle 0.54601 ( 4644) hydrogen bonds : bond 0.01953 ( 88) hydrogen bonds : angle 4.34858 ( 267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7134 (mp0) REVERT: A 379 ARG cc_start: 0.6114 (ttt180) cc_final: 0.3699 (mmp-170) REVERT: B 331 LYS cc_start: 0.8889 (mttt) cc_final: 0.8640 (mtpt) REVERT: B 340 LYS cc_start: 0.8453 (mttt) cc_final: 0.8183 (mttt) REVERT: B 342 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7082 (mp0) REVERT: B 343 LYS cc_start: 0.8091 (mptt) cc_final: 0.7667 (mppt) REVERT: B 351 GLN cc_start: 0.8338 (mt0) cc_final: 0.8095 (mt0) REVERT: B 379 ARG cc_start: 0.6368 (ttt180) cc_final: 0.5348 (mpp80) REVERT: C 342 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: C 349 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7329 (mtp180) REVERT: D 317 LYS cc_start: 0.7470 (mttp) cc_final: 0.6960 (ttmt) REVERT: D 342 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7056 (mt-10) REVERT: E 314 ASP cc_start: 0.8215 (t0) cc_final: 0.7976 (t0) REVERT: F 343 LYS cc_start: 0.8018 (mptt) cc_final: 0.7638 (mppt) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 1.5181 time to fit residues: 113.3992 Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.153517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.127357 restraints weight = 10838.042| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.94 r_work: 0.3828 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3474 Z= 0.175 Angle : 0.570 4.257 4644 Z= 0.291 Chirality : 0.050 0.139 516 Planarity : 0.003 0.027 594 Dihedral : 6.709 19.976 456 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 1.28 % Allowed : 19.23 % Favored : 79.49 % 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: -2.74 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.011 0.002 TYR E 310 PHE 0.007 0.002 PHE D 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3474) covalent geometry : angle 0.57039 ( 4644) hydrogen bonds : bond 0.02109 ( 88) hydrogen bonds : angle 4.48966 ( 267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8181 (tttt) cc_final: 0.7848 (ttmm) REVERT: A 331 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8490 (mttm) REVERT: A 342 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7128 (mp0) REVERT: A 379 ARG cc_start: 0.6028 (ttt180) cc_final: 0.3739 (mmp-170) REVERT: B 311 LYS cc_start: 0.7767 (tttt) cc_final: 0.7080 (tmmt) REVERT: B 331 LYS cc_start: 0.8918 (mttt) cc_final: 0.8676 (mtpt) REVERT: B 340 LYS cc_start: 0.8477 (mttt) cc_final: 0.8208 (mttt) REVERT: B 342 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7090 (mp0) REVERT: B 343 LYS cc_start: 0.8118 (mptt) cc_final: 0.7718 (mppt) REVERT: B 351 GLN cc_start: 0.8416 (mt0) cc_final: 0.8148 (mt0) REVERT: B 379 ARG cc_start: 0.6601 (ttt180) cc_final: 0.5369 (mpp80) REVERT: C 342 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 349 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7137 (mtp85) REVERT: D 317 LYS cc_start: 0.7436 (mttp) cc_final: 0.6933 (ttmt) REVERT: D 342 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7215 (mt-10) REVERT: E 314 ASP cc_start: 0.8238 (t0) cc_final: 0.7936 (t0) REVERT: F 311 LYS cc_start: 0.8396 (tttp) cc_final: 0.7376 (tppt) REVERT: F 370 LYS cc_start: 0.8374 (tttt) cc_final: 0.6723 (mttt) outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 1.3724 time to fit residues: 105.4635 Evaluate side-chains 74 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.149485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123586 restraints weight = 11105.128| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.92 r_work: 0.3852 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3474 Z= 0.130 Angle : 0.543 4.507 4644 Z= 0.277 Chirality : 0.050 0.135 516 Planarity : 0.003 0.029 594 Dihedral : 6.516 18.888 456 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 0.77 % Allowed : 19.49 % Favored : 79.74 % 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: -2.74 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.008 0.002 TYR D 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3474) covalent geometry : angle 0.54332 ( 4644) hydrogen bonds : bond 0.01942 ( 88) hydrogen bonds : angle 4.31657 ( 267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8165 (tttt) cc_final: 0.7769 (ttmm) REVERT: A 342 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7136 (mp0) REVERT: B 311 LYS cc_start: 0.7735 (tttt) cc_final: 0.7067 (tmmt) REVERT: B 331 LYS cc_start: 0.8892 (mttt) cc_final: 0.8652 (mtpt) REVERT: B 342 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7042 (mp0) REVERT: B 343 LYS cc_start: 0.8094 (mptt) cc_final: 0.7701 (mppt) REVERT: B 351 GLN cc_start: 0.8365 (mt0) cc_final: 0.8097 (mt0) REVERT: B 379 ARG cc_start: 0.6651 (ttt180) cc_final: 0.5474 (mpp80) REVERT: C 342 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: C 349 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7134 (mtp85) REVERT: D 317 LYS cc_start: 0.7455 (mttp) cc_final: 0.6949 (ttmt) REVERT: D 342 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7068 (mt-10) REVERT: E 314 ASP cc_start: 0.8252 (t0) cc_final: 0.7994 (t0) REVERT: F 311 LYS cc_start: 0.8435 (tttp) cc_final: 0.7400 (tppt) REVERT: F 343 LYS cc_start: 0.8025 (mptt) cc_final: 0.7668 (mppt) REVERT: F 370 LYS cc_start: 0.8362 (tttt) cc_final: 0.6707 (mttt) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 1.3367 time to fit residues: 98.7005 Evaluate side-chains 73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.149760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.124186 restraints weight = 10944.097| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.86 r_work: 0.3860 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3474 Z= 0.127 Angle : 0.529 3.729 4644 Z= 0.270 Chirality : 0.050 0.136 516 Planarity : 0.003 0.029 594 Dihedral : 6.423 18.860 456 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 0.77 % Allowed : 21.03 % Favored : 78.21 % 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: -2.78 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.008 0.002 TYR E 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3474) covalent geometry : angle 0.52940 ( 4644) hydrogen bonds : bond 0.01846 ( 88) hydrogen bonds : angle 4.27500 ( 267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7118 (mp0) REVERT: B 311 LYS cc_start: 0.7766 (tttt) cc_final: 0.7068 (tmmt) REVERT: B 331 LYS cc_start: 0.8880 (mttt) cc_final: 0.8639 (mtpt) REVERT: B 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7056 (mp0) REVERT: B 343 LYS cc_start: 0.8146 (mptt) cc_final: 0.7733 (mppt) REVERT: B 351 GLN cc_start: 0.8335 (mt0) cc_final: 0.8068 (mt0) REVERT: B 379 ARG cc_start: 0.6610 (ttt180) cc_final: 0.5440 (mpp80) REVERT: C 342 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: D 317 LYS cc_start: 0.7339 (mttp) cc_final: 0.6801 (ttmt) REVERT: D 342 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7202 (mt-10) REVERT: E 314 ASP cc_start: 0.8226 (t0) cc_final: 0.7992 (t0) REVERT: F 311 LYS cc_start: 0.8434 (tttp) cc_final: 0.7389 (tppt) REVERT: F 343 LYS cc_start: 0.8024 (mptt) cc_final: 0.7664 (mppt) REVERT: F 370 LYS cc_start: 0.8391 (tttt) cc_final: 0.6695 (mttt) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 1.3250 time to fit residues: 97.7697 Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.148786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123077 restraints weight = 11054.168| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.89 r_work: 0.3852 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3474 Z= 0.140 Angle : 0.543 4.750 4644 Z= 0.277 Chirality : 0.050 0.137 516 Planarity : 0.003 0.034 594 Dihedral : 6.467 18.859 456 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 0.77 % Allowed : 21.54 % Favored : 77.69 % 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: -2.80 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.002 TYR E 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3474) covalent geometry : angle 0.54309 ( 4644) hydrogen bonds : bond 0.01880 ( 88) hydrogen bonds : angle 4.31965 ( 267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8052 (tttt) cc_final: 0.7734 (ttmm) REVERT: A 342 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7137 (mp0) REVERT: B 311 LYS cc_start: 0.7833 (tttt) cc_final: 0.7126 (tmmt) REVERT: B 331 LYS cc_start: 0.8895 (mttt) cc_final: 0.8664 (mtpt) REVERT: B 342 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7078 (mp0) REVERT: B 343 LYS cc_start: 0.8148 (mptt) cc_final: 0.7749 (mppt) REVERT: B 351 GLN cc_start: 0.8363 (mt0) cc_final: 0.8099 (mt0) REVERT: B 379 ARG cc_start: 0.6478 (ttt180) cc_final: 0.5422 (mpp80) REVERT: C 342 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7401 (mt-10) REVERT: C 349 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7337 (mtp180) REVERT: D 317 LYS cc_start: 0.7377 (mttp) cc_final: 0.6847 (ttmt) REVERT: D 342 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7213 (mt-10) REVERT: E 314 ASP cc_start: 0.8235 (t0) cc_final: 0.7983 (t0) REVERT: F 311 LYS cc_start: 0.8456 (tttp) cc_final: 0.7420 (tppt) REVERT: F 343 LYS cc_start: 0.8010 (mptt) cc_final: 0.7674 (mppt) REVERT: F 370 LYS cc_start: 0.8415 (tttt) cc_final: 0.6733 (mttt) REVERT: F 375 LYS cc_start: 0.6351 (mttt) cc_final: 0.5982 (mmmm) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 1.3292 time to fit residues: 100.6247 Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.150955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125535 restraints weight = 10979.633| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.89 r_work: 0.3876 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3474 Z= 0.111 Angle : 0.517 3.618 4644 Z= 0.265 Chirality : 0.050 0.135 516 Planarity : 0.003 0.030 594 Dihedral : 6.274 18.380 456 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.41 % Favored : 92.36 % Rotamer: Outliers : 1.03 % Allowed : 21.28 % Favored : 77.69 % 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: -2.77 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.006 0.001 TYR E 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3474) covalent geometry : angle 0.51714 ( 4644) hydrogen bonds : bond 0.01744 ( 88) hydrogen bonds : angle 4.18078 ( 267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.42 seconds wall clock time: 58 minutes 42.02 seconds (3522.02 seconds total)