Starting phenix.real_space_refine on Sat Apr 26 22:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.map" model { file = "/net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hrf_0260/04_2025/6hrf_0260.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.06, per 1000 atoms: 0.58 Number of scatterers: 3522 At special positions: 0 Unit cell: (115.44, 118.56, 37.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 666 8.00 N 648 7.00 C 2202 6.00 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: 0.76 Conformation dependent library (CDL) restraints added in 467.0 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.632A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322 removed outlier: 7.197A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 6.810A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS C 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.691A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359 removed outlier: 7.330A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASN C 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER C 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN E 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP C 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.549A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.558A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322 removed outlier: 7.138A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.873A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.550A pdb=" N LYS B 340 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 341 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.764A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359 removed outlier: 7.381A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER D 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN F 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 369 through 371 Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378 removed outlier: 6.610A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE F 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 33 hydrogen bonds defined for protein. 99 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: 0.77 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: 1.20 - 1.32: 630 1.32 - 1.44: 788 1.44 - 1.55: 2027 1.55 - 1.67: 125 1.67 - 1.79: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" C LYS E 311 " pdb=" N PRO E 312 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.17e-02 7.31e+03 2.07e+01 bond pdb=" C LYS B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.333 1.385 -0.053 1.17e-02 7.31e+03 2.03e+01 bond pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 1.457 1.529 -0.071 1.58e-02 4.01e+03 2.03e+01 bond pdb=" C LYS A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.333 1.385 -0.053 1.17e-02 7.31e+03 2.02e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 4011 1.38 - 2.76: 519 2.76 - 4.14: 163 4.14 - 5.51: 71 5.51 - 6.89: 18 Bond angle restraints: 4782 Sorted by residual: angle pdb=" N SER F 352 " pdb=" CA SER F 352 " pdb=" C SER F 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER E 352 " pdb=" CA SER E 352 " pdb=" C SER E 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER C 352 " pdb=" CA SER C 352 " pdb=" C SER C 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER D 352 " pdb=" CA SER D 352 " pdb=" C SER D 352 " ideal model delta sigma weight residual 108.99 114.68 -5.69 1.57e+00 4.06e-01 1.31e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 1896 13.36 - 26.71: 174 26.71 - 40.06: 72 40.06 - 53.41: 24 53.41 - 66.76: 12 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" CB LYS B 353 " pdb=" CG LYS B 353 " pdb=" CD LYS B 353 " pdb=" CE LYS B 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.76 41.76 3 1.50e+01 4.44e-03 7.48e+00 dihedral pdb=" CB LYS A 353 " pdb=" CG LYS A 353 " pdb=" CD LYS A 353 " pdb=" CE LYS A 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.73 41.73 3 1.50e+01 4.44e-03 7.47e+00 dihedral pdb=" CB LYS D 353 " pdb=" CG LYS D 353 " pdb=" CD LYS D 353 " pdb=" CE LYS D 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.72 41.72 3 1.50e+01 4.44e-03 7.47e+00 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 227 0.050 - 0.099: 142 0.099 - 0.149: 81 0.149 - 0.198: 72 0.198 - 0.248: 12 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE D 328 " pdb=" N ILE D 328 " pdb=" C ILE D 328 " pdb=" CB ILE D 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE B 328 " pdb=" N ILE B 328 " pdb=" C ILE B 328 " pdb=" CB ILE B 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 368 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN E 368 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN E 368 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS E 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 368 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN A 368 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN A 368 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 368 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN B 368 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 368 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 369 " -0.015 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 2011 3.08 - 3.54: 3350 3.54 - 3.99: 5016 3.99 - 4.45: 4850 4.45 - 4.90: 9434 Nonbonded interactions: 24661 Sorted by model distance: nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.627 3.120 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.628 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.628 3.120 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.628 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.628 3.120 ... (remaining 24656 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.880 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.900 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.016 0.071 3576 Z= 1.075 Angle : 1.247 6.892 4782 Z= 0.750 Chirality : 0.093 0.248 534 Planarity : 0.010 0.038 612 Dihedral : 13.679 66.761 1374 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 362 PHE 0.027 0.008 PHE C 346 TYR 0.033 0.014 TYR C 310 ARG 0.010 0.003 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.21344 ( 33) hydrogen bonds : angle 7.35327 ( 99) covalent geometry : bond 0.01591 ( 3576) covalent geometry : angle 1.24686 ( 4782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.409 Fit side-chains REVERT: A 311 LYS cc_start: 0.8535 (mtmt) cc_final: 0.7769 (mmmt) REVERT: A 317 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8154 (ptpp) REVERT: A 349 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7108 (mtm180) REVERT: A 353 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7648 (tttm) REVERT: B 311 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8307 (mmmt) REVERT: C 317 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7508 (ptpp) REVERT: C 343 LYS cc_start: 0.8134 (mttp) cc_final: 0.7818 (ttmm) REVERT: C 349 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7740 (mtm-85) REVERT: D 327 ASN cc_start: 0.7756 (p0) cc_final: 0.7370 (p0) REVERT: E 317 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7763 (ptpp) REVERT: E 349 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7920 (mtm180) REVERT: E 361 THR cc_start: 0.9083 (m) cc_final: 0.8877 (t) REVERT: E 379 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6404 (ptt-90) REVERT: F 310 TYR cc_start: 0.8833 (t80) cc_final: 0.8616 (t80) REVERT: F 311 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8439 (mtpt) REVERT: F 327 ASN cc_start: 0.8104 (p0) cc_final: 0.7629 (p0) REVERT: F 379 ARG cc_start: 0.6578 (mtt180) cc_final: 0.5019 (mtm110) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.3169 time to fit residues: 51.2752 Evaluate side-chains 87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN C 329 HIS C 336 GLN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.146963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.121432 restraints weight = 5504.092| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.13 r_work: 0.3828 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3576 Z= 0.231 Angle : 0.688 6.420 4782 Z= 0.352 Chirality : 0.050 0.147 534 Planarity : 0.004 0.029 612 Dihedral : 5.354 13.725 474 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.74 % Allowed : 12.44 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS C 330 PHE 0.010 0.002 PHE B 378 TYR 0.015 0.002 TYR D 310 ARG 0.006 0.001 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 33) hydrogen bonds : angle 6.10548 ( 99) covalent geometry : bond 0.00515 ( 3576) covalent geometry : angle 0.68795 ( 4782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8666 (mtmt) cc_final: 0.7941 (mmtm) REVERT: A 317 LYS cc_start: 0.8578 (ptpt) cc_final: 0.7918 (ptpp) REVERT: A 349 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7475 (mtm180) REVERT: A 353 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7431 (tppt) REVERT: B 311 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8351 (mmtt) REVERT: B 327 ASN cc_start: 0.8035 (p0) cc_final: 0.7811 (p0) REVERT: B 336 GLN cc_start: 0.7972 (pp30) cc_final: 0.7577 (pp30) REVERT: B 351 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7768 (tm-30) REVERT: C 338 GLU cc_start: 0.7549 (mp0) cc_final: 0.7028 (tm-30) REVERT: C 349 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.7173 (mtm-85) REVERT: D 327 ASN cc_start: 0.8093 (p0) cc_final: 0.7559 (p0) REVERT: E 342 GLU cc_start: 0.3387 (pm20) cc_final: 0.2702 (pm20) REVERT: E 343 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7311 (mtmm) REVERT: E 349 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7600 (mtm180) REVERT: E 379 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6638 (ptt-90) REVERT: F 311 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8716 (mtpt) REVERT: F 327 ASN cc_start: 0.8399 (p0) cc_final: 0.8108 (p0) REVERT: F 379 ARG cc_start: 0.6703 (mtt180) cc_final: 0.5928 (mtm180) outliers start: 7 outliers final: 6 residues processed: 110 average time/residue: 0.2554 time to fit residues: 31.7416 Evaluate side-chains 106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.143373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.120185 restraints weight = 5592.548| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.03 r_work: 0.3770 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 3576 Z= 0.368 Angle : 0.819 6.067 4782 Z= 0.415 Chirality : 0.052 0.143 534 Planarity : 0.004 0.028 612 Dihedral : 6.055 18.194 474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.48 % Allowed : 15.42 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 330 PHE 0.023 0.003 PHE B 378 TYR 0.027 0.003 TYR A 310 ARG 0.005 0.001 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 33) hydrogen bonds : angle 5.62412 ( 99) covalent geometry : bond 0.00815 ( 3576) covalent geometry : angle 0.81909 ( 4782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8189 (mmtm) REVERT: A 317 LYS cc_start: 0.8650 (ptpt) cc_final: 0.8020 (ptpp) REVERT: A 338 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 349 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7416 (mtm180) REVERT: B 311 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8340 (mmtt) REVERT: C 336 GLN cc_start: 0.7924 (mp10) cc_final: 0.7718 (mp10) REVERT: C 338 GLU cc_start: 0.7726 (mp0) cc_final: 0.7216 (tm-30) REVERT: C 349 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7355 (mtm-85) REVERT: D 327 ASN cc_start: 0.8125 (p0) cc_final: 0.7546 (p0) REVERT: D 336 GLN cc_start: 0.8249 (mp10) cc_final: 0.7865 (mp-120) REVERT: E 343 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7509 (ttmm) REVERT: E 348 ASP cc_start: 0.8066 (m-30) cc_final: 0.7487 (p0) REVERT: E 349 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7727 (mtm180) REVERT: E 372 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8145 (mm-30) REVERT: E 379 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6630 (ptt-90) REVERT: F 311 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8730 (mtpt) REVERT: F 336 GLN cc_start: 0.7973 (mp10) cc_final: 0.7732 (mp-120) outliers start: 14 outliers final: 9 residues processed: 119 average time/residue: 0.2217 time to fit residues: 30.6565 Evaluate side-chains 110 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.118477 restraints weight = 5438.537| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.03 r_work: 0.3799 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3576 Z= 0.150 Angle : 0.667 8.546 4782 Z= 0.318 Chirality : 0.048 0.132 534 Planarity : 0.003 0.023 612 Dihedral : 4.964 16.106 474 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.48 % Allowed : 19.15 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.007 0.001 PHE B 378 TYR 0.019 0.003 TYR E 310 ARG 0.005 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02356 ( 33) hydrogen bonds : angle 5.45087 ( 99) covalent geometry : bond 0.00334 ( 3576) covalent geometry : angle 0.66709 ( 4782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8754 (mtmt) cc_final: 0.7999 (mmtm) REVERT: A 317 LYS cc_start: 0.8611 (ptpt) cc_final: 0.7949 (ptpp) REVERT: A 338 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6358 (tm-30) REVERT: A 349 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7355 (mtm180) REVERT: B 311 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8273 (mmtt) REVERT: C 336 GLN cc_start: 0.7957 (mp10) cc_final: 0.7703 (mp10) REVERT: C 338 GLU cc_start: 0.7625 (mp0) cc_final: 0.7047 (tm-30) REVERT: C 341 SER cc_start: 0.8139 (m) cc_final: 0.7796 (t) REVERT: C 349 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7057 (mtm-85) REVERT: D 327 ASN cc_start: 0.8142 (p0) cc_final: 0.7668 (p0) REVERT: D 336 GLN cc_start: 0.8309 (mp10) cc_final: 0.8083 (mp-120) REVERT: E 336 GLN cc_start: 0.8225 (mp10) cc_final: 0.7979 (mp10) REVERT: E 349 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7564 (mtm180) REVERT: E 379 ARG cc_start: 0.7561 (mtt180) cc_final: 0.6603 (ptt-90) REVERT: F 311 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8622 (mtpt) REVERT: F 316 SER cc_start: 0.9462 (p) cc_final: 0.9208 (p) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.2023 time to fit residues: 27.8109 Evaluate side-chains 113 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.115323 restraints weight = 5607.256| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.00 r_work: 0.3757 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3576 Z= 0.245 Angle : 0.727 6.992 4782 Z= 0.350 Chirality : 0.049 0.141 534 Planarity : 0.003 0.025 612 Dihedral : 5.228 16.011 474 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.73 % Allowed : 19.15 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.018 0.002 PHE B 378 TYR 0.019 0.003 TYR E 310 ARG 0.004 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 33) hydrogen bonds : angle 5.43635 ( 99) covalent geometry : bond 0.00544 ( 3576) covalent geometry : angle 0.72704 ( 4782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.402 Fit side-chains REVERT: A 311 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8079 (mmtm) REVERT: A 317 LYS cc_start: 0.8610 (ptpt) cc_final: 0.7975 (ptpp) REVERT: A 338 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6439 (tm-30) REVERT: A 349 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7185 (mtm180) REVERT: B 311 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8312 (mmtt) REVERT: B 337 VAL cc_start: 0.8896 (t) cc_final: 0.8351 (t) REVERT: C 336 GLN cc_start: 0.7971 (mp10) cc_final: 0.7762 (mp10) REVERT: C 338 GLU cc_start: 0.7617 (mp0) cc_final: 0.7167 (tm-30) REVERT: C 349 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7120 (mtm-85) REVERT: D 327 ASN cc_start: 0.8216 (p0) cc_final: 0.7639 (p0) REVERT: D 336 GLN cc_start: 0.8397 (mp10) cc_final: 0.7797 (mp-120) REVERT: E 336 GLN cc_start: 0.8231 (mp10) cc_final: 0.7967 (mp10) REVERT: E 342 GLU cc_start: 0.3162 (OUTLIER) cc_final: 0.2406 (pm20) REVERT: E 349 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7595 (mtm180) REVERT: F 311 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8676 (mtpt) REVERT: F 327 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7606 (p0) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.2013 time to fit residues: 27.7423 Evaluate side-chains 121 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 327 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.136503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.114376 restraints weight = 5679.008| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.99 r_work: 0.3741 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3576 Z= 0.265 Angle : 0.754 7.750 4782 Z= 0.363 Chirality : 0.049 0.150 534 Planarity : 0.003 0.027 612 Dihedral : 5.202 16.012 474 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.48 % Allowed : 19.90 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.018 0.002 PHE B 378 TYR 0.016 0.002 TYR A 310 ARG 0.004 0.001 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02671 ( 33) hydrogen bonds : angle 5.29822 ( 99) covalent geometry : bond 0.00589 ( 3576) covalent geometry : angle 0.75425 ( 4782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.402 Fit side-chains REVERT: A 311 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8062 (mmtm) REVERT: A 317 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8025 (ptpp) REVERT: A 338 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6464 (tm-30) REVERT: A 349 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7163 (mtm180) REVERT: B 311 LYS cc_start: 0.9114 (mtmt) cc_final: 0.8319 (mmtt) REVERT: C 336 GLN cc_start: 0.7987 (mp10) cc_final: 0.7758 (mp10) REVERT: C 338 GLU cc_start: 0.7584 (mp0) cc_final: 0.7190 (tm-30) REVERT: C 349 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7085 (mtm-85) REVERT: D 327 ASN cc_start: 0.8203 (p0) cc_final: 0.7694 (p0) REVERT: D 336 GLN cc_start: 0.8186 (mp10) cc_final: 0.7972 (mp-120) REVERT: D 349 ARG cc_start: 0.6298 (tpm170) cc_final: 0.5620 (ttp-110) REVERT: E 336 GLN cc_start: 0.8250 (mp10) cc_final: 0.8037 (mp10) REVERT: E 349 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7610 (mtm180) REVERT: F 311 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8667 (mtpt) REVERT: F 327 ASN cc_start: 0.7851 (p0) cc_final: 0.7576 (p0) REVERT: F 349 ARG cc_start: 0.2145 (ppt170) cc_final: 0.1734 (ppt170) outliers start: 18 outliers final: 18 residues processed: 116 average time/residue: 0.2025 time to fit residues: 27.3973 Evaluate side-chains 122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 339 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.137586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.115791 restraints weight = 5534.736| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.93 r_work: 0.3739 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3576 Z= 0.292 Angle : 0.776 6.987 4782 Z= 0.375 Chirality : 0.050 0.161 534 Planarity : 0.004 0.027 612 Dihedral : 5.293 18.746 474 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.48 % Allowed : 21.64 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.021 0.002 PHE B 378 TYR 0.016 0.002 TYR A 310 ARG 0.004 0.001 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 33) hydrogen bonds : angle 5.31482 ( 99) covalent geometry : bond 0.00648 ( 3576) covalent geometry : angle 0.77602 ( 4782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.444 Fit side-chains REVERT: A 311 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8120 (mmtm) REVERT: A 317 LYS cc_start: 0.8638 (ptpt) cc_final: 0.8048 (ptpp) REVERT: A 338 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6556 (tm-30) REVERT: A 349 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7185 (mtm180) REVERT: B 311 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8346 (mmtt) REVERT: B 336 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6770 (tm-30) REVERT: C 336 GLN cc_start: 0.8110 (mp10) cc_final: 0.7856 (mp10) REVERT: C 338 GLU cc_start: 0.7759 (mp0) cc_final: 0.7300 (tm-30) REVERT: C 349 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7100 (mtm-85) REVERT: D 327 ASN cc_start: 0.8339 (p0) cc_final: 0.7845 (p0) REVERT: D 336 GLN cc_start: 0.8351 (mp10) cc_final: 0.7919 (mp-120) REVERT: D 345 ASP cc_start: 0.7635 (m-30) cc_final: 0.6362 (p0) REVERT: D 351 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6659 (mp10) REVERT: E 349 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7621 (mtm180) REVERT: F 311 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8767 (mtpt) REVERT: F 327 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7656 (p0) REVERT: F 349 ARG cc_start: 0.2324 (ppt170) cc_final: 0.1863 (ppt170) outliers start: 18 outliers final: 17 residues processed: 114 average time/residue: 0.2066 time to fit residues: 27.4015 Evaluate side-chains 121 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 20.0000 chunk 28 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.142162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.120684 restraints weight = 5415.438| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.85 r_work: 0.3812 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3576 Z= 0.159 Angle : 0.695 7.114 4782 Z= 0.333 Chirality : 0.048 0.164 534 Planarity : 0.003 0.034 612 Dihedral : 4.621 15.656 474 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.23 % Allowed : 22.64 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.008 0.001 PHE B 378 TYR 0.014 0.002 TYR D 310 ARG 0.009 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01980 ( 33) hydrogen bonds : angle 5.17185 ( 99) covalent geometry : bond 0.00360 ( 3576) covalent geometry : angle 0.69462 ( 4782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.397 Fit side-chains REVERT: A 311 LYS cc_start: 0.8816 (mtmt) cc_final: 0.7974 (mmtm) REVERT: A 317 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7961 (ptpp) REVERT: A 338 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6521 (tm-30) REVERT: A 349 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7195 (mtm180) REVERT: B 311 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8276 (mmtt) REVERT: C 336 GLN cc_start: 0.8202 (mp10) cc_final: 0.7795 (mp10) REVERT: C 338 GLU cc_start: 0.7778 (mp0) cc_final: 0.7246 (tm-30) REVERT: C 349 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7048 (mtm-85) REVERT: D 319 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8892 (t) REVERT: D 327 ASN cc_start: 0.8319 (p0) cc_final: 0.7915 (p0) REVERT: D 336 GLN cc_start: 0.8249 (mp10) cc_final: 0.7796 (mp-120) REVERT: D 345 ASP cc_start: 0.7704 (m-30) cc_final: 0.6448 (p0) REVERT: D 351 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6862 (mp10) REVERT: E 349 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7594 (mtm180) REVERT: F 311 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8799 (mtpt) REVERT: F 316 SER cc_start: 0.9499 (p) cc_final: 0.9266 (p) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.1914 time to fit residues: 25.2755 Evaluate side-chains 111 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.0060 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.138500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.116484 restraints weight = 5378.194| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.83 r_work: 0.3779 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.7437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3576 Z= 0.216 Angle : 0.745 9.037 4782 Z= 0.364 Chirality : 0.049 0.169 534 Planarity : 0.004 0.043 612 Dihedral : 4.828 16.917 474 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.99 % Allowed : 23.63 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.014 0.002 PHE B 378 TYR 0.015 0.003 TYR F 310 ARG 0.007 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02380 ( 33) hydrogen bonds : angle 5.15694 ( 99) covalent geometry : bond 0.00488 ( 3576) covalent geometry : angle 0.74474 ( 4782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.438 Fit side-chains REVERT: A 311 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8008 (mmtm) REVERT: A 317 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8023 (ptpp) REVERT: A 338 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6632 (tm-30) REVERT: A 349 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7199 (mtm180) REVERT: B 311 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8356 (mmtm) REVERT: C 336 GLN cc_start: 0.8189 (mp10) cc_final: 0.7844 (mp10) REVERT: C 338 GLU cc_start: 0.7789 (mp0) cc_final: 0.7271 (tm-30) REVERT: C 349 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7112 (mtm-85) REVERT: D 319 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8927 (t) REVERT: D 324 SER cc_start: 0.8246 (p) cc_final: 0.8005 (m) REVERT: D 325 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7940 (mm) REVERT: D 327 ASN cc_start: 0.8335 (p0) cc_final: 0.7933 (p0) REVERT: D 336 GLN cc_start: 0.8207 (mp10) cc_final: 0.7833 (mp-120) REVERT: D 338 GLU cc_start: 0.8556 (mp0) cc_final: 0.8328 (mp0) REVERT: D 345 ASP cc_start: 0.7635 (m-30) cc_final: 0.6373 (p0) REVERT: D 351 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6812 (mp10) REVERT: E 349 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7631 (mtm180) REVERT: F 311 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8781 (mtpt) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.1883 time to fit residues: 24.3530 Evaluate side-chains 114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.120237 restraints weight = 5414.891| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.91 r_work: 0.3809 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3576 Z= 0.166 Angle : 0.720 8.377 4782 Z= 0.350 Chirality : 0.048 0.176 534 Planarity : 0.004 0.035 612 Dihedral : 4.486 15.203 474 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.24 % Allowed : 24.63 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.009 0.001 PHE B 378 TYR 0.016 0.003 TYR F 310 ARG 0.007 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01934 ( 33) hydrogen bonds : angle 5.09320 ( 99) covalent geometry : bond 0.00384 ( 3576) covalent geometry : angle 0.71976 ( 4782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.439 Fit side-chains REVERT: A 311 LYS cc_start: 0.8846 (mtmt) cc_final: 0.7962 (mmtm) REVERT: A 317 LYS cc_start: 0.8581 (ptpt) cc_final: 0.7976 (ptpp) REVERT: A 338 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6607 (tm-30) REVERT: A 349 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7238 (mtm180) REVERT: B 311 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8316 (mmtt) REVERT: C 336 GLN cc_start: 0.8188 (mp10) cc_final: 0.7856 (mp10) REVERT: C 338 GLU cc_start: 0.7753 (mp0) cc_final: 0.7173 (tm-30) REVERT: C 349 ARG cc_start: 0.7737 (mtt-85) cc_final: 0.7102 (mtm-85) REVERT: D 319 THR cc_start: 0.9214 (p) cc_final: 0.8907 (t) REVERT: D 324 SER cc_start: 0.8255 (p) cc_final: 0.7998 (m) REVERT: D 325 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7649 (mt) REVERT: D 327 ASN cc_start: 0.8323 (p0) cc_final: 0.7982 (p0) REVERT: D 336 GLN cc_start: 0.8111 (mp10) cc_final: 0.7697 (mp-120) REVERT: D 345 ASP cc_start: 0.7668 (m-30) cc_final: 0.6444 (p0) REVERT: D 351 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6967 (mp10) REVERT: D 380 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7209 (mp0) REVERT: E 310 TYR cc_start: 0.8911 (t80) cc_final: 0.8538 (t80) REVERT: E 349 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7596 (mtm180) REVERT: F 316 SER cc_start: 0.9519 (p) cc_final: 0.9292 (p) outliers start: 9 outliers final: 8 residues processed: 107 average time/residue: 0.1922 time to fit residues: 24.5055 Evaluate side-chains 109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.115394 restraints weight = 5502.570| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.86 r_work: 0.3764 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3576 Z= 0.240 Angle : 0.754 8.421 4782 Z= 0.368 Chirality : 0.049 0.181 534 Planarity : 0.004 0.039 612 Dihedral : 4.790 15.300 474 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.74 % Allowed : 23.88 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.015 0.002 PHE B 378 TYR 0.015 0.003 TYR A 310 ARG 0.009 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02501 ( 33) hydrogen bonds : angle 5.12331 ( 99) covalent geometry : bond 0.00543 ( 3576) covalent geometry : angle 0.75411 ( 4782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.96 seconds wall clock time: 37 minutes 56.06 seconds (2276.06 seconds total)