Starting phenix.real_space_refine on Sun Mar 10 17:37:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_0260.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_0260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_0260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_0260.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/03_2024/6hrf_0260.pdb" } 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 Residue "A ARG 379": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.29, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 563.8 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: 0.43 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: 0.73 Time building geometry restraints manager: 1.23 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: 102.98 - 108.67: 204 108.67 - 114.37: 2082 114.37 - 120.06: 834 120.06 - 125.76: 1620 125.76 - 131.45: 42 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 2.520 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.628 2.520 ... (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 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: 0.810 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: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- 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= 1.101 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.414 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: 0.3012 time to fit residues: 48.8895 Evaluate side-chains 87 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN E 336 GLN F 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4354 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= 0.335 Angle : 0.661 6.127 4782 Z= 0.337 Chirality : 0.049 0.147 534 Planarity : 0.004 0.030 612 Dihedral : 5.131 12.770 474 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.49 % Allowed : 11.69 % 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: -3.73 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 330 PHE 0.011 0.002 PHE B 378 TYR 0.014 0.002 TYR D 310 ARG 0.006 0.000 ARG C 379 *********************** 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 fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8272 (mmtm) REVERT: A 317 LYS cc_start: 0.8715 (ptpt) cc_final: 0.8186 (ptpp) REVERT: A 338 GLU cc_start: 0.7266 (mp0) cc_final: 0.6947 (tm-30) REVERT: A 349 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7809 (mtm180) REVERT: B 311 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8417 (mmtt) REVERT: C 338 GLU cc_start: 0.8143 (mp0) cc_final: 0.7309 (tm-30) REVERT: C 349 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7473 (mtm-85) REVERT: D 327 ASN cc_start: 0.8024 (p0) cc_final: 0.7634 (p0) REVERT: E 342 GLU cc_start: 0.2778 (pm20) cc_final: 0.2325 (pm20) REVERT: E 343 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7145 (mtmm) REVERT: E 349 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7841 (mtm180) REVERT: E 379 ARG cc_start: 0.7421 (mtt180) cc_final: 0.6688 (ptt-90) REVERT: F 311 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8650 (mtpt) REVERT: F 327 ASN cc_start: 0.8318 (p0) cc_final: 0.7947 (p0) REVERT: F 379 ARG cc_start: 0.6700 (mtt180) cc_final: 0.5801 (mtm180) outliers start: 10 outliers final: 9 residues processed: 109 average time/residue: 0.2510 time to fit residues: 30.9956 Evaluate side-chains 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 373 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 Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 368 ASN C 329 HIS ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3576 Z= 0.304 Angle : 0.649 5.527 4782 Z= 0.320 Chirality : 0.048 0.137 534 Planarity : 0.004 0.034 612 Dihedral : 5.000 14.719 474 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.23 % Allowed : 15.42 % Favored : 81.34 % 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: -3.61 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 330 PHE 0.011 0.002 PHE F 346 TYR 0.022 0.003 TYR A 310 ARG 0.006 0.000 ARG C 379 *********************** 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 120 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8249 (mmtm) REVERT: A 317 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8206 (ptpp) REVERT: A 349 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7843 (mtm180) REVERT: B 311 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8372 (mmtt) REVERT: B 336 GLN cc_start: 0.7834 (pp30) cc_final: 0.7165 (pp30) REVERT: C 336 GLN cc_start: 0.8600 (mp10) cc_final: 0.8178 (mp10) REVERT: C 338 GLU cc_start: 0.8002 (mp0) cc_final: 0.7265 (tm-30) REVERT: C 349 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.7481 (mtm-85) REVERT: D 327 ASN cc_start: 0.8038 (p0) cc_final: 0.7651 (p0) REVERT: E 342 GLU cc_start: 0.2732 (pm20) cc_final: 0.2469 (pm20) REVERT: E 343 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7201 (mtmm) REVERT: E 349 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7765 (mtm180) REVERT: E 379 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6745 (ptt-90) REVERT: F 311 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8738 (mtpt) REVERT: F 316 SER cc_start: 0.9358 (p) cc_final: 0.9091 (p) REVERT: F 327 ASN cc_start: 0.8327 (p0) cc_final: 0.7989 (p0) REVERT: F 379 ARG cc_start: 0.7032 (mtt180) cc_final: 0.5975 (mtm180) outliers start: 13 outliers final: 9 residues processed: 113 average time/residue: 0.2420 time to fit residues: 31.1410 Evaluate side-chains 110 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 359 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.068 3576 Z= 0.698 Angle : 0.874 8.150 4782 Z= 0.445 Chirality : 0.055 0.144 534 Planarity : 0.005 0.029 612 Dihedral : 6.461 18.361 474 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.98 % Allowed : 17.66 % 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: -3.90 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.032 0.003 PHE B 378 TYR 0.023 0.003 TYR A 310 ARG 0.006 0.001 ARG C 379 *********************** 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 121 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.385 Fit side-chains REVERT: A 311 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8381 (mmtm) REVERT: A 317 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8194 (ptpp) REVERT: A 349 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7208 (mtm180) REVERT: B 311 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8414 (mmtt) REVERT: C 338 GLU cc_start: 0.7856 (mp0) cc_final: 0.7359 (tm-30) REVERT: C 349 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7269 (mtm-85) REVERT: D 327 ASN cc_start: 0.8119 (p0) cc_final: 0.7733 (p0) REVERT: E 349 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7767 (mtm180) REVERT: E 379 ARG cc_start: 0.7764 (mtt180) cc_final: 0.6700 (ptt-90) REVERT: F 311 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8760 (mtpt) REVERT: F 327 ASN cc_start: 0.8252 (p0) cc_final: 0.7875 (p0) REVERT: F 338 GLU cc_start: 0.8603 (mp0) cc_final: 0.8260 (pm20) REVERT: F 380 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6659 (mp0) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.1926 time to fit residues: 25.5784 Evaluate side-chains 113 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 B residue 319 THR Chi-restraints excluded: chain B residue 359 ASN 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 D residue 377 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 359 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3576 Z= 0.175 Angle : 0.633 8.059 4782 Z= 0.300 Chirality : 0.047 0.144 534 Planarity : 0.003 0.023 612 Dihedral : 4.589 16.172 474 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.99 % Allowed : 22.39 % 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: -3.70 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 329 PHE 0.007 0.001 PHE D 346 TYR 0.016 0.003 TYR A 310 ARG 0.004 0.000 ARG F 349 *********************** 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 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8280 (mmtm) REVERT: A 317 LYS cc_start: 0.8699 (ptpt) cc_final: 0.8167 (ptpp) REVERT: A 349 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7451 (mtm180) REVERT: B 311 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8330 (mmtm) REVERT: C 336 GLN cc_start: 0.8560 (mp10) cc_final: 0.8228 (mp10) REVERT: C 338 GLU cc_start: 0.7876 (mp0) cc_final: 0.7223 (tm-30) REVERT: C 349 ARG cc_start: 0.7795 (mtt-85) cc_final: 0.7308 (mtm-85) REVERT: D 327 ASN cc_start: 0.8041 (p0) cc_final: 0.7790 (p0) REVERT: E 343 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7369 (ttmm) REVERT: E 348 ASP cc_start: 0.8228 (t0) cc_final: 0.7282 (p0) REVERT: E 349 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7733 (mtm180) REVERT: E 379 ARG cc_start: 0.7553 (mtt180) cc_final: 0.6835 (ptt-90) REVERT: F 311 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8674 (mtpt) REVERT: F 327 ASN cc_start: 0.7939 (p0) cc_final: 0.7668 (p0) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.2189 time to fit residues: 25.6386 Evaluate side-chains 102 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 ASN Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- 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** B 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3576 Z= 0.271 Angle : 0.658 8.108 4782 Z= 0.311 Chirality : 0.047 0.160 534 Planarity : 0.003 0.033 612 Dihedral : 4.630 15.233 474 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.49 % Allowed : 23.13 % Favored : 74.38 % 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: -3.70 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.011 0.001 PHE B 378 TYR 0.017 0.003 TYR A 310 ARG 0.007 0.001 ARG D 349 *********************** 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 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.427 Fit side-chains REVERT: A 311 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8291 (mmtm) REVERT: A 317 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8204 (ptpp) REVERT: A 349 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7403 (mtm180) REVERT: B 311 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8344 (mmtt) REVERT: C 338 GLU cc_start: 0.7897 (mp0) cc_final: 0.7339 (tm-30) REVERT: C 349 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7328 (mtm-85) REVERT: D 327 ASN cc_start: 0.8161 (p0) cc_final: 0.7784 (p0) REVERT: E 343 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7456 (ttmm) REVERT: E 348 ASP cc_start: 0.8121 (t0) cc_final: 0.7262 (p0) REVERT: E 349 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7713 (mtm180) REVERT: E 379 ARG cc_start: 0.7639 (mtt180) cc_final: 0.6800 (ptt-90) REVERT: F 327 ASN cc_start: 0.8072 (p0) cc_final: 0.7771 (p0) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.2265 time to fit residues: 26.5930 Evaluate side-chains 102 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 327 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3576 Z= 0.276 Angle : 0.675 7.799 4782 Z= 0.320 Chirality : 0.047 0.167 534 Planarity : 0.003 0.031 612 Dihedral : 4.654 15.681 474 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.73 % Allowed : 23.38 % Favored : 72.89 % 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: -3.69 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.011 0.001 PHE B 378 TYR 0.016 0.003 TYR A 310 ARG 0.008 0.001 ARG D 349 *********************** 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 111 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.435 Fit side-chains REVERT: A 311 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8248 (mmtm) REVERT: A 317 LYS cc_start: 0.8725 (ptpt) cc_final: 0.8205 (ptpp) REVERT: A 349 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7438 (mtm180) REVERT: B 311 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8346 (mmtt) REVERT: C 336 GLN cc_start: 0.8625 (mp10) cc_final: 0.8231 (mp10) REVERT: C 338 GLU cc_start: 0.7890 (mp0) cc_final: 0.7334 (tm-30) REVERT: C 349 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7290 (mtm-85) REVERT: D 327 ASN cc_start: 0.8042 (p0) cc_final: 0.7725 (p0) REVERT: D 380 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6482 (mp0) REVERT: E 343 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7449 (ttmm) REVERT: E 348 ASP cc_start: 0.8253 (t0) cc_final: 0.7313 (p0) REVERT: E 349 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7709 (mtm180) REVERT: E 379 ARG cc_start: 0.7640 (mtt180) cc_final: 0.6808 (ptt-90) REVERT: F 327 ASN cc_start: 0.8053 (p0) cc_final: 0.7764 (p0) REVERT: F 380 GLU cc_start: 0.6835 (mp0) cc_final: 0.6496 (mp0) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2100 time to fit residues: 25.2499 Evaluate side-chains 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 E residue 319 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 overall best weight: 2.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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** F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3576 Z= 0.220 Angle : 0.647 7.637 4782 Z= 0.306 Chirality : 0.047 0.169 534 Planarity : 0.003 0.036 612 Dihedral : 4.372 14.985 474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.74 % Allowed : 24.13 % 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: -3.62 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.008 0.001 PHE B 378 TYR 0.016 0.003 TYR F 310 ARG 0.008 0.001 ARG D 349 *********************** 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 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.423 Fit side-chains REVERT: A 311 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8228 (mmtm) REVERT: A 317 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8158 (ptpp) REVERT: A 349 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7498 (mtm180) REVERT: B 311 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8296 (mmtt) REVERT: B 337 VAL cc_start: 0.8609 (t) cc_final: 0.8335 (t) REVERT: C 336 GLN cc_start: 0.8630 (mp10) cc_final: 0.8210 (mp10) REVERT: C 338 GLU cc_start: 0.7887 (mp0) cc_final: 0.7341 (tm-30) REVERT: C 349 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7316 (mtm-85) REVERT: D 327 ASN cc_start: 0.8047 (p0) cc_final: 0.7805 (p0) REVERT: D 380 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6387 (mp0) REVERT: E 310 TYR cc_start: 0.8549 (t80) cc_final: 0.8314 (t80) REVERT: E 348 ASP cc_start: 0.8166 (t0) cc_final: 0.7294 (p0) REVERT: E 349 ARG cc_start: 0.8133 (mtt-85) cc_final: 0.7725 (mtm180) REVERT: E 379 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6849 (ptt-90) REVERT: F 327 ASN cc_start: 0.7949 (p0) cc_final: 0.7662 (p0) REVERT: F 380 GLU cc_start: 0.6843 (mp0) cc_final: 0.6520 (mp0) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.1908 time to fit residues: 22.8374 Evaluate side-chains 103 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 319 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3576 Z= 0.322 Angle : 0.679 7.588 4782 Z= 0.326 Chirality : 0.048 0.170 534 Planarity : 0.003 0.040 612 Dihedral : 4.673 15.283 474 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.73 % Allowed : 22.14 % 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: -3.64 (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 0.002 0.001 HIS C 330 PHE 0.014 0.002 PHE B 378 TYR 0.016 0.003 TYR A 310 ARG 0.008 0.001 ARG D 349 *********************** 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 110 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.444 Fit side-chains REVERT: A 311 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8305 (mmtm) REVERT: A 317 LYS cc_start: 0.8684 (ptpt) cc_final: 0.8193 (ptpp) REVERT: A 349 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7311 (mtm180) REVERT: B 311 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8291 (mmtt) REVERT: C 336 GLN cc_start: 0.8636 (mp10) cc_final: 0.8226 (mp10) REVERT: C 338 GLU cc_start: 0.7895 (mp0) cc_final: 0.7368 (tm-30) REVERT: C 349 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7263 (mtm-85) REVERT: D 327 ASN cc_start: 0.8084 (p0) cc_final: 0.7810 (p0) REVERT: E 348 ASP cc_start: 0.8188 (t0) cc_final: 0.6951 (p0) REVERT: E 349 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7737 (mtm180) REVERT: E 379 ARG cc_start: 0.7664 (mtt180) cc_final: 0.6828 (ptt-90) REVERT: F 327 ASN cc_start: 0.8031 (p0) cc_final: 0.7708 (p0) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.1886 time to fit residues: 22.8773 Evaluate side-chains 107 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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** B 368 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3576 Z= 0.255 Angle : 0.669 7.619 4782 Z= 0.319 Chirality : 0.048 0.172 534 Planarity : 0.003 0.030 612 Dihedral : 4.482 15.288 474 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.48 % Allowed : 23.13 % 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: -3.59 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 330 PHE 0.010 0.001 PHE B 378 TYR 0.016 0.003 TYR F 310 ARG 0.007 0.001 ARG D 349 ********************** 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 fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.467 Fit side-chains REVERT: A 311 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8255 (mmtm) REVERT: A 317 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8207 (ptpp) REVERT: A 349 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7358 (mtm180) REVERT: B 311 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8299 (mmtm) REVERT: B 337 VAL cc_start: 0.8553 (t) cc_final: 0.8129 (t) REVERT: C 336 GLN cc_start: 0.8649 (mp10) cc_final: 0.8208 (mp10) REVERT: C 338 GLU cc_start: 0.7884 (mp0) cc_final: 0.7362 (tm-30) REVERT: C 349 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7269 (mtm-85) REVERT: D 380 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6151 (mp0) REVERT: E 348 ASP cc_start: 0.8211 (t0) cc_final: 0.6987 (p0) REVERT: E 349 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7719 (mtm180) REVERT: E 379 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6877 (ptt-90) REVERT: F 327 ASN cc_start: 0.7963 (p0) cc_final: 0.7725 (p0) outliers start: 14 outliers final: 12 residues processed: 103 average time/residue: 0.1904 time to fit residues: 23.0692 Evaluate side-chains 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 A residue 352 SER Chi-restraints excluded: chain B residue 319 THR 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 E residue 319 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.115830 restraints weight = 5592.766| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.97 r_work: 0.3760 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.7313 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= 0.342 Angle : 0.703 7.461 4782 Z= 0.340 Chirality : 0.048 0.172 534 Planarity : 0.003 0.031 612 Dihedral : 4.777 15.511 474 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 23.13 % 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: -3.60 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.016 0.002 PHE B 378 TYR 0.024 0.004 TYR E 310 ARG 0.007 0.001 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.60 seconds wall clock time: 22 minutes 54.70 seconds (1374.70 seconds total)