Starting phenix.real_space_refine on Wed Sep 17 08:10:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422.map" model { file = "/net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbm_44422/09_2025/9bbm_44422_neut.cif" } resolution = 3.2 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= 0.002 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 630 1.98 5 H 3558 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6966 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 6966 At special positions: 0 Unit cell: (143.1, 78.44, 37.1, 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 630 8.00 N 630 7.00 C 2142 6.00 H 3558 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: 0.51 Conformation dependent library (CDL) restraints added in 218.2 milliseconds Enol-peptide restraints added in 715.3 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, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 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 319 through 321 removed outlier: 6.474A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) 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 339 removed outlier: 6.405A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.858A pdb=" N SER C 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS A 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY E 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.779A 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 removed outlier: 6.567A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.667A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 378 removed outlier: 6.594A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 309 through 310 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 329 through 330 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.080A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 354 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.505A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.213A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 375 through 378 Processing sheet with id=AC2, first strand: chain 'D' and resid 320 through 321 removed outlier: 6.577A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 48 hydrogen bonds defined for protein. 144 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: 1.30 Time building geometry restraints manager: 0.70 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: 3552 1.12 - 1.30: 567 1.30 - 1.47: 1169 1.47 - 1.64: 1726 1.64 - 1.82: 6 Bond restraints: 7020 Sorted by residual: bond pdb=" NE2 HIS A 362 " pdb=" HE2 HIS A 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N GLN A 307 " pdb=" H GLN A 307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER C 356 " pdb=" H SER C 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE F 308 " pdb=" H ILE F 308 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU B 338 " pdb=" H GLU B 338 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 10412 2.46 - 4.92: 1825 4.92 - 7.38: 506 7.38 - 9.84: 46 9.84 - 12.30: 9 Bond angle restraints: 12798 Sorted by residual: angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 120.08 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.32 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.68e+01 ... (remaining 12793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 2797 16.53 - 33.06: 248 33.06 - 49.59: 85 49.59 - 66.12: 91 66.12 - 82.66: 7 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 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+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 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL E 339 " pdb=" C VAL E 339 " pdb=" N LYS E 340 " pdb=" CA LYS E 340 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 3225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 296 0.086 - 0.172: 172 0.172 - 0.258: 44 0.258 - 0.343: 5 0.343 - 0.429: 5 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA ASP C 348 " pdb=" N ASP C 348 " pdb=" C ASP C 348 " pdb=" CB ASP C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA PRO C 364 " pdb=" N PRO C 364 " pdb=" C PRO C 364 " pdb=" CB PRO C 364 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" C PRO E 364 " pdb=" CB PRO E 364 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 519 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.163 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.126 2.00e-02 2.50e+03 7.13e-02 1.14e+02 pdb=" CG HIS D 330 " 0.068 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 HIS D 330 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.116 2.00e-02 2.50e+03 6.51e-02 9.53e+01 pdb=" CG HIS C 330 " -0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 HIS C 330 " 0.077 2.00e-02 2.50e+03 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 492 2.17 - 2.78: 11929 2.78 - 3.38: 18796 3.38 - 3.99: 24703 3.99 - 4.60: 35640 Nonbonded interactions: 91560 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.564 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.617 2.450 ... (remaining 91555 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: 3.870 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.830 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.012 0.039 3462 Z= 0.730 Angle : 2.054 8.969 4632 Z= 1.328 Chirality : 0.109 0.429 522 Planarity : 0.013 0.105 588 Dihedral : 13.726 82.656 1332 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 4.86 % Allowed : 12.73 % Favored : 82.41 % Rotamer: Outliers : 0.51 % Allowed : 4.87 % Favored : 94.62 % Cbeta Deviations : 1.03 % 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: -3.91 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 379 TYR 0.146 0.038 TYR C 310 PHE 0.041 0.011 PHE A 378 HIS 0.013 0.004 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.01155 ( 3462) covalent geometry : angle 2.05427 ( 4632) hydrogen bonds : bond 0.10317 ( 48) hydrogen bonds : angle 7.13691 ( 144) *********************** 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 118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.208 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: A 349 ARG cc_start: 0.5028 (mtt-85) cc_final: 0.4036 (ppt170) REVERT: C 342 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5154 (mp0) REVERT: C 349 ARG cc_start: 0.5618 (mtt-85) cc_final: 0.5391 (mtt90) REVERT: C 369 LYS cc_start: 0.6313 (mttt) cc_final: 0.6028 (mtmm) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.3213 time to fit residues: 41.8255 Evaluate side-chains 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 336 GLN D 351 GLN E 336 GLN F 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.156805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.146612 restraints weight = 15439.523| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.10 r_work: 0.4257 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3462 Z= 0.171 Angle : 0.760 6.295 4632 Z= 0.397 Chirality : 0.053 0.156 522 Planarity : 0.004 0.050 588 Dihedral : 8.406 43.423 459 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.34 % Favored : 87.73 % Rotamer: Outliers : 1.54 % Allowed : 10.26 % Favored : 88.21 % 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: -3.27 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.019 0.004 TYR C 310 PHE 0.011 0.001 PHE C 378 HIS 0.007 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3462) covalent geometry : angle 0.76015 ( 4632) hydrogen bonds : bond 0.02598 ( 48) hydrogen bonds : angle 5.78472 ( 144) *********************** 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 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6517 (mtt180) cc_final: 0.4815 (ppt170) REVERT: C 342 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: C 369 LYS cc_start: 0.8132 (mttt) cc_final: 0.7663 (mtmm) REVERT: E 311 LYS cc_start: 0.5752 (tppt) cc_final: 0.5451 (tppt) REVERT: E 369 LYS cc_start: 0.8221 (mtmt) cc_final: 0.8007 (ttpt) REVERT: F 321 LYS cc_start: 0.6922 (tppt) cc_final: 0.6639 (tppt) outliers start: 6 outliers final: 2 residues processed: 84 average time/residue: 0.3084 time to fit residues: 28.7437 Evaluate side-chains 65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.159577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.149902 restraints weight = 14868.332| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.08 r_work: 0.4303 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3462 Z= 0.113 Angle : 0.634 5.482 4632 Z= 0.325 Chirality : 0.051 0.150 522 Planarity : 0.004 0.044 588 Dihedral : 7.253 45.006 459 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.26 % Favored : 89.81 % Rotamer: Outliers : 1.54 % Allowed : 11.54 % Favored : 86.92 % 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: -3.16 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.019 0.004 TYR C 310 PHE 0.008 0.001 PHE C 378 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3462) covalent geometry : angle 0.63375 ( 4632) hydrogen bonds : bond 0.02086 ( 48) hydrogen bonds : angle 5.07924 ( 144) *********************** 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 73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.209 Fit side-chains REVERT: D 336 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 311 LYS cc_start: 0.5811 (tppt) cc_final: 0.5506 (tppt) REVERT: E 369 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8068 (ttpt) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.2778 time to fit residues: 21.1998 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.157178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.147503 restraints weight = 14892.602| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.03 r_work: 0.4277 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3462 Z= 0.124 Angle : 0.590 4.785 4632 Z= 0.304 Chirality : 0.050 0.153 522 Planarity : 0.004 0.041 588 Dihedral : 6.860 47.476 459 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.93 % Allowed : 10.19 % Favored : 88.89 % Rotamer: Outliers : 1.28 % Allowed : 11.79 % Favored : 86.92 % 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: -3.18 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.017 0.004 TYR C 310 PHE 0.009 0.002 PHE C 378 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3462) covalent geometry : angle 0.58989 ( 4632) hydrogen bonds : bond 0.01990 ( 48) hydrogen bonds : angle 4.83159 ( 144) *********************** 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 64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7602 (ttmt) REVERT: A 324 SER cc_start: 0.8798 (m) cc_final: 0.8440 (t) REVERT: D 336 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8008 (tm-30) REVERT: D 351 GLN cc_start: 0.7622 (tt0) cc_final: 0.7358 (tt0) REVERT: E 311 LYS cc_start: 0.5856 (tppt) cc_final: 0.5598 (tppt) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.2178 time to fit residues: 15.4859 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.156623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.147119 restraints weight = 15118.700| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.04 r_work: 0.4247 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3462 Z= 0.120 Angle : 0.566 5.583 4632 Z= 0.290 Chirality : 0.049 0.143 522 Planarity : 0.003 0.041 588 Dihedral : 6.587 47.885 459 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.49 % Favored : 89.58 % Rotamer: Outliers : 2.56 % Allowed : 11.03 % Favored : 86.41 % 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: -3.21 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.014 0.003 TYR C 310 PHE 0.007 0.001 PHE C 378 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3462) covalent geometry : angle 0.56586 ( 4632) hydrogen bonds : bond 0.01736 ( 48) hydrogen bonds : angle 4.71835 ( 144) *********************** 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 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7627 (tttt) REVERT: A 324 SER cc_start: 0.8751 (m) cc_final: 0.8392 (t) REVERT: C 369 LYS cc_start: 0.8333 (mttt) cc_final: 0.7921 (mttp) REVERT: D 336 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 311 LYS cc_start: 0.5811 (tppt) cc_final: 0.5557 (tppt) REVERT: E 357 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (tt) REVERT: E 370 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8232 (tttp) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.2123 time to fit residues: 15.4364 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.152553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.143239 restraints weight = 15280.920| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.01 r_work: 0.4219 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3462 Z= 0.173 Angle : 0.623 8.196 4632 Z= 0.316 Chirality : 0.050 0.144 522 Planarity : 0.004 0.043 588 Dihedral : 6.753 49.354 459 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.34 % Favored : 87.73 % Rotamer: Outliers : 2.05 % Allowed : 12.05 % Favored : 85.90 % 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: -3.27 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.019 0.005 TYR A 310 PHE 0.011 0.002 PHE D 378 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3462) covalent geometry : angle 0.62264 ( 4632) hydrogen bonds : bond 0.01811 ( 48) hydrogen bonds : angle 4.77282 ( 144) *********************** 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 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7702 (tttt) REVERT: A 324 SER cc_start: 0.8665 (m) cc_final: 0.8294 (t) REVERT: C 369 LYS cc_start: 0.8330 (mttt) cc_final: 0.7869 (mtmm) REVERT: D 317 LYS cc_start: 0.7059 (mptt) cc_final: 0.6538 (tttt) REVERT: E 311 LYS cc_start: 0.6000 (tppt) cc_final: 0.5770 (tppt) REVERT: E 357 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8560 (tt) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.2170 time to fit residues: 13.9978 Evaluate side-chains 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.153051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.143764 restraints weight = 15147.720| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.04 r_work: 0.4227 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3462 Z= 0.144 Angle : 0.585 6.187 4632 Z= 0.299 Chirality : 0.049 0.144 522 Planarity : 0.004 0.040 588 Dihedral : 6.597 50.068 459 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.95 % Favored : 89.12 % Rotamer: Outliers : 1.54 % Allowed : 13.33 % Favored : 85.13 % 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: -3.27 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.015 0.004 TYR A 310 PHE 0.008 0.001 PHE D 378 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3462) covalent geometry : angle 0.58540 ( 4632) hydrogen bonds : bond 0.01663 ( 48) hydrogen bonds : angle 4.73124 ( 144) *********************** 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 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8745 (m) cc_final: 0.8378 (t) REVERT: C 369 LYS cc_start: 0.8344 (mttt) cc_final: 0.7866 (mtmm) REVERT: D 317 LYS cc_start: 0.7000 (mptt) cc_final: 0.6476 (tttt) REVERT: E 311 LYS cc_start: 0.5960 (tppt) cc_final: 0.5747 (tppt) REVERT: E 357 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8508 (tt) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.2293 time to fit residues: 14.5704 Evaluate side-chains 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.150795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.141697 restraints weight = 15503.729| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.96 r_work: 0.4173 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4087 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3462 Z= 0.216 Angle : 0.639 5.674 4632 Z= 0.331 Chirality : 0.051 0.146 522 Planarity : 0.004 0.040 588 Dihedral : 6.900 50.532 459 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.50 % Favored : 86.57 % Rotamer: Outliers : 1.79 % Allowed : 12.82 % Favored : 85.38 % 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: -3.37 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.022 0.005 TYR A 310 PHE 0.013 0.002 PHE D 378 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 3462) covalent geometry : angle 0.63866 ( 4632) hydrogen bonds : bond 0.01848 ( 48) hydrogen bonds : angle 4.88699 ( 144) *********************** 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 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7992 (ttmt) REVERT: A 324 SER cc_start: 0.8684 (m) cc_final: 0.8359 (t) REVERT: C 369 LYS cc_start: 0.8388 (mttt) cc_final: 0.7928 (mtmm) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.2359 time to fit residues: 15.0377 Evaluate side-chains 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.155846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.146644 restraints weight = 14969.870| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.03 r_work: 0.4258 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3462 Z= 0.097 Angle : 0.559 6.395 4632 Z= 0.282 Chirality : 0.049 0.146 522 Planarity : 0.004 0.040 588 Dihedral : 6.400 51.757 459 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.26 % Favored : 89.81 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.25 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.009 0.002 TYR D 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3462) covalent geometry : angle 0.55907 ( 4632) hydrogen bonds : bond 0.01620 ( 48) hydrogen bonds : angle 4.72387 ( 144) *********************** 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 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8329 (mttt) cc_final: 0.7879 (mtmm) REVERT: D 317 LYS cc_start: 0.7038 (mptt) cc_final: 0.6584 (ttpt) REVERT: E 357 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.2276 time to fit residues: 14.2151 Evaluate side-chains 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.159386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.150328 restraints weight = 14715.930| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.02 r_work: 0.4299 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3462 Z= 0.088 Angle : 0.535 6.168 4632 Z= 0.268 Chirality : 0.048 0.141 522 Planarity : 0.004 0.040 588 Dihedral : 6.033 50.965 459 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.03 % Favored : 90.05 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.10 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.010 0.002 TYR C 310 PHE 0.007 0.001 PHE B 378 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3462) covalent geometry : angle 0.53498 ( 4632) hydrogen bonds : bond 0.01540 ( 48) hydrogen bonds : angle 4.64347 ( 144) ********************** 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 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8355 (mttt) cc_final: 0.7865 (mtmm) REVERT: D 336 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 338 GLU cc_start: 0.7573 (tt0) cc_final: 0.7361 (tp30) REVERT: E 319 THR cc_start: 0.7548 (t) cc_final: 0.7243 (p) REVERT: E 357 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8483 (tt) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.2118 time to fit residues: 14.4229 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.157292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.148236 restraints weight = 14844.495| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.00 r_work: 0.4276 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4188 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3462 Z= 0.108 Angle : 0.539 6.187 4632 Z= 0.272 Chirality : 0.049 0.137 522 Planarity : 0.004 0.040 588 Dihedral : 6.079 51.280 459 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.95 % Favored : 89.12 % Rotamer: Outliers : 1.28 % Allowed : 13.85 % Favored : 84.87 % 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: -3.09 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.012 0.003 TYR C 310 PHE 0.006 0.001 PHE B 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3462) covalent geometry : angle 0.53946 ( 4632) hydrogen bonds : bond 0.01393 ( 48) hydrogen bonds : angle 4.66426 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.69 seconds wall clock time: 41 minutes 29.92 seconds (2489.92 seconds total)