Starting phenix.real_space_refine on Fri Apr 5 13:24:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oth_17179/04_2024/8oth_17179.pdb" } resolution = 3.4 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.89, per 1000 atoms: 0.66 Number of scatterers: 2870 At special positions: 0 Unit cell: (135.464, 109.032, 33.04, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 1.01 Conformation dependent library (CDL) restraints added in 533.0 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.991A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.819A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 319 through 328 removed outlier: 6.803A pdb=" N THR A 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N CYS D 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS A 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER D 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY A 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLY D 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU A 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ILE D 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.481A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 342 through 345 removed outlier: 6.926A pdb=" N LYS A 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A 342 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP E 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.460A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.781A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.498A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.991A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.820A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 328 removed outlier: 6.803A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS C 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER C 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY B 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLY C 326 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU B 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ILE C 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB4, first strand: chain 'B' and resid 342 through 345 removed outlier: 6.926A pdb=" N LYS B 343 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'B' and resid 369 through 373 removed outlier: 6.780A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 376 through 378 40 hydrogen bonds defined for protein. 120 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: 0.56 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 727 1.34 - 1.46: 657 1.46 - 1.58: 1526 1.58 - 1.70: 0 1.70 - 1.82: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.21e+00 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.00e+00 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.92e+00 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.80e+00 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.75e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 102.20 - 108.58: 370 108.58 - 114.96: 1500 114.96 - 121.34: 1256 121.34 - 127.73: 754 127.73 - 134.11: 20 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C HIS D 362 " pdb=" CA HIS D 362 " pdb=" CB HIS D 362 " ideal model delta sigma weight residual 110.22 119.02 -8.80 1.67e+00 3.59e-01 2.78e+01 angle pdb=" C HIS B 362 " pdb=" CA HIS B 362 " pdb=" CB HIS B 362 " ideal model delta sigma weight residual 110.22 119.02 -8.80 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS C 362 " pdb=" CA HIS C 362 " pdb=" CB HIS C 362 " ideal model delta sigma weight residual 110.22 119.01 -8.79 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS A 362 " pdb=" CA HIS A 362 " pdb=" CB HIS A 362 " ideal model delta sigma weight residual 110.22 119.00 -8.78 1.67e+00 3.59e-01 2.77e+01 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 110.22 119.00 -8.78 1.67e+00 3.59e-01 2.76e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1540 14.74 - 29.48: 190 29.48 - 44.21: 40 44.21 - 58.95: 5 58.95 - 73.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA VAL B 318 " pdb=" C VAL B 318 " pdb=" N THR B 319 " pdb=" CA THR B 319 " ideal model delta harmonic sigma weight residual 180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 162 0.052 - 0.103: 166 0.103 - 0.155: 82 0.155 - 0.206: 25 0.206 - 0.258: 5 Chirality restraints: 440 Sorted by residual: 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 2.69 -0.26 2.00e-01 2.50e+01 1.66e+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 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE A 328 " pdb=" N ILE A 328 " pdb=" C ILE A 328 " pdb=" CB ILE A 328 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C VAL D 363 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL D 363 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO D 364 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 363 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL B 363 " -0.075 2.00e-02 2.50e+03 pdb=" O VAL B 363 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B 364 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 363 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL A 363 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 363 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO A 364 " -0.025 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 598 2.81 - 3.33: 2681 3.33 - 3.85: 4409 3.85 - 4.38: 4732 4.38 - 4.90: 8981 Nonbonded interactions: 21401 Sorted by model distance: nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.287 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.287 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.287 2.520 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.287 2.520 nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.287 2.520 ... (remaining 21396 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 12.500 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.640 Find NCS groups from input model: 0.170 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.009 0.041 2915 Z= 0.583 Angle : 1.555 8.805 3900 Z= 1.013 Chirality : 0.092 0.258 440 Planarity : 0.011 0.054 495 Dihedral : 14.035 73.685 1120 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.52 % Allowed : 10.61 % Favored : 87.88 % 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: -4.34 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS C 329 PHE 0.017 0.004 PHE D 346 TYR 0.035 0.013 TYR E 310 ARG 0.004 0.002 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.359 Fit side-chains REVERT: A 347 LYS cc_start: 0.8220 (mttt) cc_final: 0.7703 (mptt) REVERT: A 369 LYS cc_start: 0.8381 (mttt) cc_final: 0.7869 (mtpt) REVERT: A 378 PHE cc_start: 0.8163 (t80) cc_final: 0.7901 (t80) REVERT: B 311 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7060 (mmmt) REVERT: B 321 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6294 (tttt) REVERT: B 347 LYS cc_start: 0.8459 (mttt) cc_final: 0.7975 (mptt) REVERT: B 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7743 (mmm160) REVERT: B 369 LYS cc_start: 0.8429 (mttt) cc_final: 0.7920 (mtpt) REVERT: C 321 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7317 (ttmt) REVERT: C 349 ARG cc_start: 0.8804 (mtt180) cc_final: 0.7529 (pmt-80) REVERT: C 369 LYS cc_start: 0.8546 (mttt) cc_final: 0.8133 (mtpt) REVERT: D 321 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7238 (ttmt) REVERT: D 347 LYS cc_start: 0.8559 (mttt) cc_final: 0.8321 (mptt) REVERT: D 349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7559 (pmt-80) REVERT: D 369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8040 (mtmt) REVERT: E 311 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7126 (mmmt) REVERT: E 321 LYS cc_start: 0.6808 (ttmt) cc_final: 0.6372 (ttpt) REVERT: E 347 LYS cc_start: 0.8389 (mttt) cc_final: 0.7987 (mptt) REVERT: E 349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7761 (mmp-170) REVERT: E 369 LYS cc_start: 0.8373 (mttt) cc_final: 0.7844 (mtpt) outliers start: 5 outliers final: 0 residues processed: 75 average time/residue: 0.2838 time to fit residues: 23.5830 Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 362 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS E 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2915 Z= 0.255 Angle : 0.616 4.937 3900 Z= 0.317 Chirality : 0.050 0.130 440 Planarity : 0.004 0.028 495 Dihedral : 5.946 20.826 385 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.42 % Allowed : 13.64 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.98 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.006 0.001 PHE E 346 TYR 0.016 0.004 TYR A 310 ARG 0.002 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.347 Fit side-chains REVERT: A 375 LYS cc_start: 0.8035 (tttt) cc_final: 0.7566 (mttt) REVERT: B 311 LYS cc_start: 0.7657 (mtmt) cc_final: 0.7052 (mmtt) REVERT: B 347 LYS cc_start: 0.8275 (mttt) cc_final: 0.7831 (mptt) REVERT: B 369 LYS cc_start: 0.8335 (mttt) cc_final: 0.7857 (mtpt) REVERT: B 375 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7576 (mttt) REVERT: C 349 ARG cc_start: 0.8780 (mtt180) cc_final: 0.7412 (pmt-80) REVERT: C 369 LYS cc_start: 0.8296 (mttt) cc_final: 0.7909 (mtpt) REVERT: C 375 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8167 (mttt) REVERT: D 321 LYS cc_start: 0.7473 (ttmt) cc_final: 0.7181 (ttmt) REVERT: D 347 LYS cc_start: 0.8521 (mttt) cc_final: 0.8310 (mptt) REVERT: D 369 LYS cc_start: 0.8403 (mttt) cc_final: 0.7898 (mtpt) REVERT: D 375 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8084 (mttt) REVERT: E 311 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7178 (mmtt) REVERT: E 347 LYS cc_start: 0.8296 (mttt) cc_final: 0.7860 (mptt) REVERT: E 349 ARG cc_start: 0.8824 (mtt180) cc_final: 0.7796 (mmm160) REVERT: E 369 LYS cc_start: 0.8067 (mttt) cc_final: 0.7654 (mtpt) REVERT: E 375 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7862 (mttt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.2902 time to fit residues: 21.3744 Evaluate side-chains 62 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2915 Z= 0.213 Angle : 0.540 4.805 3900 Z= 0.278 Chirality : 0.048 0.123 440 Planarity : 0.004 0.049 495 Dihedral : 4.960 18.725 385 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.18 % 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: -3.32 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 330 PHE 0.005 0.001 PHE E 346 TYR 0.017 0.004 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.338 Fit side-chains REVERT: A 375 LYS cc_start: 0.8101 (tttt) cc_final: 0.7683 (mttt) REVERT: B 311 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7194 (mmtt) REVERT: B 347 LYS cc_start: 0.8200 (mttt) cc_final: 0.7786 (mptt) REVERT: B 349 ARG cc_start: 0.8894 (mtt180) cc_final: 0.7857 (mmp-170) REVERT: B 369 LYS cc_start: 0.8417 (mttt) cc_final: 0.7916 (mtpt) REVERT: B 375 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7664 (mttt) REVERT: C 347 LYS cc_start: 0.8386 (mptt) cc_final: 0.8068 (mptt) REVERT: C 349 ARG cc_start: 0.8917 (mtt180) cc_final: 0.7565 (pmt-80) REVERT: C 369 LYS cc_start: 0.8364 (mttt) cc_final: 0.7929 (mtpt) REVERT: C 375 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8190 (mttt) REVERT: D 321 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7219 (ttmt) REVERT: D 347 LYS cc_start: 0.8463 (mttt) cc_final: 0.8261 (mptt) REVERT: D 369 LYS cc_start: 0.8407 (mttt) cc_final: 0.7937 (mtpt) REVERT: D 375 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8114 (mttt) REVERT: E 311 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7137 (mmtt) REVERT: E 347 LYS cc_start: 0.8287 (mttt) cc_final: 0.7819 (mptt) REVERT: E 348 ASP cc_start: 0.8900 (t70) cc_final: 0.8489 (t70) REVERT: E 349 ARG cc_start: 0.8923 (mtt180) cc_final: 0.7869 (mmm160) REVERT: E 369 LYS cc_start: 0.8101 (mttt) cc_final: 0.7685 (mtpt) REVERT: E 375 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7899 (mttt) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.2813 time to fit residues: 21.2278 Evaluate side-chains 64 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2915 Z= 0.447 Angle : 0.685 7.405 3900 Z= 0.360 Chirality : 0.051 0.146 440 Planarity : 0.006 0.055 495 Dihedral : 5.666 22.127 385 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.33 % Allowed : 22.12 % Favored : 74.55 % 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: -3.33 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 330 PHE 0.006 0.002 PHE B 346 TYR 0.016 0.005 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.330 Fit side-chains REVERT: A 375 LYS cc_start: 0.8093 (tttt) cc_final: 0.7678 (mttt) REVERT: B 311 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7160 (mmtt) REVERT: B 347 LYS cc_start: 0.8334 (mttt) cc_final: 0.7852 (mptt) REVERT: B 348 ASP cc_start: 0.9060 (t70) cc_final: 0.8739 (t70) REVERT: B 349 ARG cc_start: 0.8841 (mtt180) cc_final: 0.7839 (mmm160) REVERT: B 369 LYS cc_start: 0.8535 (mttt) cc_final: 0.8004 (mtpt) REVERT: B 375 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7635 (mttt) REVERT: B 379 ARG cc_start: 0.7760 (tmt-80) cc_final: 0.7258 (ttp80) REVERT: C 321 LYS cc_start: 0.7330 (ttmt) cc_final: 0.7091 (ttmt) REVERT: C 347 LYS cc_start: 0.8387 (mptt) cc_final: 0.8010 (mptt) REVERT: C 349 ARG cc_start: 0.8927 (mtt180) cc_final: 0.7482 (pmt-80) REVERT: C 369 LYS cc_start: 0.8488 (mttt) cc_final: 0.8103 (mtpt) REVERT: D 347 LYS cc_start: 0.8490 (mttt) cc_final: 0.8057 (mptt) REVERT: D 369 LYS cc_start: 0.8580 (mttt) cc_final: 0.8143 (mtpt) REVERT: D 375 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8136 (mttt) REVERT: E 311 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7083 (mmtt) REVERT: E 347 LYS cc_start: 0.8386 (mttt) cc_final: 0.7895 (mptt) REVERT: E 348 ASP cc_start: 0.9006 (t70) cc_final: 0.8590 (t70) REVERT: E 349 ARG cc_start: 0.8934 (mtt180) cc_final: 0.7882 (mmm160) REVERT: E 369 LYS cc_start: 0.8293 (mttt) cc_final: 0.7796 (mtpt) REVERT: E 375 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7882 (mttt) outliers start: 11 outliers final: 10 residues processed: 61 average time/residue: 0.3260 time to fit residues: 21.8234 Evaluate side-chains 64 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 0.0040 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2915 Z= 0.169 Angle : 0.549 8.735 3900 Z= 0.267 Chirality : 0.047 0.118 440 Planarity : 0.004 0.048 495 Dihedral : 4.652 17.323 385 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.64 % Allowed : 22.42 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.00 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.003 0.001 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.357 Fit side-chains REVERT: A 348 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8719 (t70) REVERT: A 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7638 (mttt) REVERT: B 311 LYS cc_start: 0.7621 (mtmt) cc_final: 0.7062 (mmtt) REVERT: B 347 LYS cc_start: 0.8138 (mttt) cc_final: 0.7746 (mptt) REVERT: B 348 ASP cc_start: 0.8988 (t70) cc_final: 0.8674 (t70) REVERT: B 349 ARG cc_start: 0.8884 (mtt180) cc_final: 0.7827 (mmm160) REVERT: B 369 LYS cc_start: 0.8527 (mttt) cc_final: 0.7999 (mtpt) REVERT: B 375 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7649 (mttt) REVERT: B 379 ARG cc_start: 0.7715 (tmt-80) cc_final: 0.7265 (ttp80) REVERT: C 347 LYS cc_start: 0.8375 (mptt) cc_final: 0.8014 (mptt) REVERT: C 369 LYS cc_start: 0.8429 (mttt) cc_final: 0.8038 (mtpt) REVERT: C 375 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8175 (mttt) REVERT: D 322 CYS cc_start: 0.8611 (t) cc_final: 0.8409 (t) REVERT: D 369 LYS cc_start: 0.8513 (mttt) cc_final: 0.7986 (mtpt) REVERT: D 375 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8126 (mttt) REVERT: E 311 LYS cc_start: 0.7618 (mtmt) cc_final: 0.7062 (mmtt) REVERT: E 347 LYS cc_start: 0.8302 (mttt) cc_final: 0.7868 (mptt) REVERT: E 349 ARG cc_start: 0.9003 (mtt180) cc_final: 0.7883 (mmm160) REVERT: E 369 LYS cc_start: 0.8294 (mttt) cc_final: 0.7809 (mtpt) REVERT: E 375 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7913 (mttt) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.2867 time to fit residues: 19.1974 Evaluate side-chains 62 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2915 Z= 0.334 Angle : 0.600 5.909 3900 Z= 0.314 Chirality : 0.049 0.128 440 Planarity : 0.005 0.047 495 Dihedral : 5.060 19.027 385 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.64 % Allowed : 23.33 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.94 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 330 PHE 0.005 0.001 PHE D 346 TYR 0.015 0.004 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.345 Fit side-chains REVERT: A 348 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8758 (t70) REVERT: A 369 LYS cc_start: 0.8739 (mttt) cc_final: 0.8146 (mtpt) REVERT: A 375 LYS cc_start: 0.8065 (tttt) cc_final: 0.7680 (mttt) REVERT: B 311 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7180 (mmtt) REVERT: B 347 LYS cc_start: 0.8244 (mttt) cc_final: 0.7792 (mptt) REVERT: B 348 ASP cc_start: 0.9035 (t70) cc_final: 0.8688 (t70) REVERT: B 349 ARG cc_start: 0.8851 (mtt180) cc_final: 0.7872 (mmp-170) REVERT: B 369 LYS cc_start: 0.8606 (mttt) cc_final: 0.8076 (mtpt) REVERT: B 375 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7647 (mttt) REVERT: B 379 ARG cc_start: 0.7734 (tmt-80) cc_final: 0.7300 (ttp80) REVERT: C 321 LYS cc_start: 0.7315 (ttmt) cc_final: 0.7091 (ttmt) REVERT: C 347 LYS cc_start: 0.8370 (mptt) cc_final: 0.7964 (mptt) REVERT: C 349 ARG cc_start: 0.8943 (mtt180) cc_final: 0.7505 (pmt-80) REVERT: C 369 LYS cc_start: 0.8535 (mttt) cc_final: 0.8117 (mtpt) REVERT: D 322 CYS cc_start: 0.8651 (t) cc_final: 0.8430 (t) REVERT: D 369 LYS cc_start: 0.8591 (mttt) cc_final: 0.8101 (mtpt) REVERT: D 375 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8117 (mttt) REVERT: E 311 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7100 (mmtt) REVERT: E 347 LYS cc_start: 0.8376 (mttt) cc_final: 0.7914 (mptt) REVERT: E 349 ARG cc_start: 0.8934 (mtt180) cc_final: 0.7918 (mmm160) REVERT: E 369 LYS cc_start: 0.8358 (mttt) cc_final: 0.7939 (mtpt) REVERT: E 375 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7839 (mttt) outliers start: 12 outliers final: 11 residues processed: 64 average time/residue: 0.3388 time to fit residues: 23.8370 Evaluate side-chains 70 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2915 Z= 0.109 Angle : 0.494 8.735 3900 Z= 0.240 Chirality : 0.047 0.117 440 Planarity : 0.004 0.056 495 Dihedral : 4.153 15.211 385 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.73 % Allowed : 24.24 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.72 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.379 Fit side-chains REVERT: A 347 LYS cc_start: 0.7955 (mttm) cc_final: 0.7501 (mptt) REVERT: A 348 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8660 (t70) REVERT: A 369 LYS cc_start: 0.8709 (mttt) cc_final: 0.8085 (mtpt) REVERT: A 375 LYS cc_start: 0.8026 (tttt) cc_final: 0.7638 (mttt) REVERT: B 311 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7137 (mmtt) REVERT: B 347 LYS cc_start: 0.8050 (mttt) cc_final: 0.7668 (mptt) REVERT: B 348 ASP cc_start: 0.8952 (t70) cc_final: 0.8637 (t70) REVERT: B 349 ARG cc_start: 0.8870 (mtt180) cc_final: 0.7780 (mmm160) REVERT: B 369 LYS cc_start: 0.8563 (mttt) cc_final: 0.8027 (mtpt) REVERT: B 375 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7658 (mttt) REVERT: B 379 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7269 (ttp80) REVERT: C 347 LYS cc_start: 0.8341 (mptt) cc_final: 0.8000 (mptt) REVERT: C 369 LYS cc_start: 0.8495 (mttt) cc_final: 0.8067 (mtpt) REVERT: C 375 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8198 (mttt) REVERT: D 369 LYS cc_start: 0.8494 (mttt) cc_final: 0.8013 (mtpt) REVERT: D 375 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8110 (mttt) REVERT: E 311 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7018 (mmtt) REVERT: E 347 LYS cc_start: 0.8255 (mttt) cc_final: 0.7822 (mptt) REVERT: E 349 ARG cc_start: 0.8973 (mtt180) cc_final: 0.7834 (mmm160) REVERT: E 369 LYS cc_start: 0.8392 (mttt) cc_final: 0.7849 (mtpt) REVERT: E 375 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7916 (mttt) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.3049 time to fit residues: 18.8129 Evaluate side-chains 58 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2915 Z= 0.162 Angle : 0.499 5.954 3900 Z= 0.247 Chirality : 0.047 0.119 440 Planarity : 0.004 0.051 495 Dihedral : 4.174 15.510 385 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.42 % Allowed : 25.15 % Favored : 72.42 % 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: -2.60 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 330 PHE 0.004 0.001 PHE D 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.361 Fit side-chains REVERT: A 347 LYS cc_start: 0.7982 (mttm) cc_final: 0.7516 (mptt) REVERT: A 348 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8703 (t70) REVERT: A 369 LYS cc_start: 0.8701 (mttt) cc_final: 0.8084 (mtpt) REVERT: A 375 LYS cc_start: 0.8050 (tttt) cc_final: 0.7658 (mttt) REVERT: B 311 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7242 (mmtt) REVERT: B 347 LYS cc_start: 0.8092 (mttt) cc_final: 0.7671 (mptt) REVERT: B 349 ARG cc_start: 0.8863 (mtt180) cc_final: 0.7791 (mmm160) REVERT: B 369 LYS cc_start: 0.8579 (mttt) cc_final: 0.8043 (mtpt) REVERT: B 375 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7663 (mttt) REVERT: B 379 ARG cc_start: 0.7707 (tmt-80) cc_final: 0.7301 (ttp80) REVERT: C 347 LYS cc_start: 0.8348 (mptt) cc_final: 0.7979 (mptt) REVERT: C 369 LYS cc_start: 0.8526 (mttt) cc_final: 0.8104 (mtpt) REVERT: C 375 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8192 (mttt) REVERT: D 375 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8115 (mttt) REVERT: E 311 LYS cc_start: 0.7681 (mtmt) cc_final: 0.7067 (mmtt) REVERT: E 347 LYS cc_start: 0.8296 (mttt) cc_final: 0.7856 (mptt) REVERT: E 349 ARG cc_start: 0.8965 (mtt180) cc_final: 0.7872 (mmm160) REVERT: E 369 LYS cc_start: 0.8430 (mttt) cc_final: 0.7880 (mtpt) REVERT: E 375 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7919 (mttt) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.3279 time to fit residues: 19.4749 Evaluate side-chains 59 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2915 Z= 0.301 Angle : 0.608 8.858 3900 Z= 0.300 Chirality : 0.049 0.160 440 Planarity : 0.004 0.048 495 Dihedral : 4.643 17.737 385 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.73 % Allowed : 26.06 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.60 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.005 0.001 PHE D 346 TYR 0.013 0.004 TYR E 310 ARG 0.000 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.343 Fit side-chains REVERT: A 348 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8730 (t70) REVERT: A 369 LYS cc_start: 0.8717 (mttt) cc_final: 0.8109 (mtpt) REVERT: A 375 LYS cc_start: 0.8063 (tttt) cc_final: 0.7647 (mttt) REVERT: B 311 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7256 (mmtt) REVERT: B 347 LYS cc_start: 0.8189 (mttt) cc_final: 0.7725 (mptt) REVERT: B 348 ASP cc_start: 0.9047 (t70) cc_final: 0.8765 (t70) REVERT: B 369 LYS cc_start: 0.8628 (mttt) cc_final: 0.8084 (mtpt) REVERT: B 375 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7656 (mttt) REVERT: B 379 ARG cc_start: 0.7659 (tmt-80) cc_final: 0.7248 (ttp80) REVERT: C 321 LYS cc_start: 0.7279 (ttmt) cc_final: 0.7058 (ttmt) REVERT: C 347 LYS cc_start: 0.8350 (mptt) cc_final: 0.7934 (mptt) REVERT: C 369 LYS cc_start: 0.8576 (mttt) cc_final: 0.8142 (mtpt) REVERT: C 375 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8179 (mttt) REVERT: E 311 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7124 (mmtt) REVERT: E 347 LYS cc_start: 0.8400 (mttt) cc_final: 0.7964 (mptt) REVERT: E 349 ARG cc_start: 0.8936 (mtt180) cc_final: 0.7924 (mmm160) REVERT: E 369 LYS cc_start: 0.8432 (mttt) cc_final: 0.7898 (mtpt) REVERT: E 375 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7859 (mttt) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.2978 time to fit residues: 18.9558 Evaluate side-chains 63 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2915 Z= 0.202 Angle : 0.568 10.062 3900 Z= 0.272 Chirality : 0.048 0.144 440 Planarity : 0.004 0.059 495 Dihedral : 4.428 16.591 385 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.73 % Allowed : 26.06 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.004 0.001 PHE D 346 TYR 0.013 0.003 TYR E 310 ARG 0.000 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.312 Fit side-chains REVERT: A 348 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8711 (t70) REVERT: A 369 LYS cc_start: 0.8702 (mttt) cc_final: 0.8102 (mtpt) REVERT: A 375 LYS cc_start: 0.8049 (tttt) cc_final: 0.7670 (mttt) REVERT: B 311 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7236 (mmtt) REVERT: B 347 LYS cc_start: 0.8168 (mttt) cc_final: 0.7707 (mptt) REVERT: B 349 ARG cc_start: 0.8786 (mtt180) cc_final: 0.7765 (mmm160) REVERT: B 369 LYS cc_start: 0.8638 (mttt) cc_final: 0.8102 (mtpt) REVERT: B 379 ARG cc_start: 0.7678 (tmt-80) cc_final: 0.7260 (ttp80) REVERT: C 321 LYS cc_start: 0.7247 (ttmt) cc_final: 0.7034 (ttmt) REVERT: C 347 LYS cc_start: 0.8342 (mptt) cc_final: 0.7952 (mptt) REVERT: C 369 LYS cc_start: 0.8599 (mttt) cc_final: 0.8153 (mtpt) REVERT: C 375 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8182 (mmtt) REVERT: D 375 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8143 (mttt) REVERT: E 311 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7112 (mmtt) REVERT: E 347 LYS cc_start: 0.8358 (mttt) cc_final: 0.7921 (mptt) REVERT: E 349 ARG cc_start: 0.8954 (mtt180) cc_final: 0.7899 (mmm160) REVERT: E 369 LYS cc_start: 0.8448 (mttt) cc_final: 0.7901 (mtpt) REVERT: E 375 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7867 (mttt) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.3099 time to fit residues: 20.0735 Evaluate side-chains 63 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4893 r_free = 0.4893 target = 0.293059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.244047 restraints weight = 3450.956| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 1.77 r_work: 0.4294 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2915 Z= 0.268 Angle : 0.603 8.399 3900 Z= 0.294 Chirality : 0.049 0.163 440 Planarity : 0.004 0.054 495 Dihedral : 4.597 17.776 385 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.73 % Allowed : 25.76 % Favored : 71.52 % 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: -2.58 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.005 0.001 PHE D 346 TYR 0.013 0.004 TYR E 310 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.78 seconds wall clock time: 23 minutes 4.40 seconds (1384.40 seconds total)