Starting phenix.real_space_refine on Fri Apr 5 15:28:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otc_17174/04_2024/8otc_17174.pdb" } resolution = 3.2 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 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 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 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 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 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 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 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" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "F" 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: 2.27, per 1000 atoms: 0.66 Number of scatterers: 3444 At special positions: 0 Unit cell: (125.248, 121.952, 38.728, 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 642 8.00 N 636 7.00 C 2160 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: 1.15 Conformation dependent library (CDL) restraints added in 599.1 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.179A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.778A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 330 removed outlier: 6.767A pdb=" N SER A 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR E 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N CYS F 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER F 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY E 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLY F 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU E 325 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE F 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN E 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS F 330 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS E 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.407A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER F 341 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS E 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 353 through 357 removed outlier: 6.133A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.952A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 378 removed outlier: 6.498A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LYS B 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS A 374 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR B 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.778A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 319 through 330 removed outlier: 6.676A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER D 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY C 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N GLY D 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.407A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 353 through 357 Processing sheet with id=AB4, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AB5, first strand: chain 'C' and resid 370 through 378 67 hydrogen bonds defined for protein. 201 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: 1.27 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: 818 1.34 - 1.46: 885 1.46 - 1.58: 1789 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" C ARG D 379 " pdb=" O ARG D 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG F 379 " pdb=" O ARG F 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG E 379 " pdb=" O ARG E 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG C 379 " pdb=" O ARG C 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ARG A 379 " pdb=" O ARG A 379 " ideal model delta sigma weight residual 1.231 1.296 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 101.09 - 107.26: 150 107.26 - 113.43: 1798 113.43 - 119.59: 1164 119.59 - 125.76: 1520 125.76 - 131.93: 48 Bond angle restraints: 4680 Sorted by residual: angle pdb=" CA ASP E 348 " pdb=" CB ASP E 348 " pdb=" CG ASP E 348 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" CA ASP C 348 " pdb=" CB ASP C 348 " pdb=" CG ASP C 348 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CA ASP D 348 " pdb=" CB ASP D 348 " pdb=" CG ASP D 348 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.00e+00 1.00e+00 2.23e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.25: 1824 13.25 - 26.50: 240 26.50 - 39.75: 66 39.75 - 53.00: 0 53.00 - 66.26: 6 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY E 365 " pdb=" C GLY E 365 " pdb=" N GLY E 366 " pdb=" CA GLY E 366 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 177 0.040 - 0.079: 136 0.079 - 0.118: 144 0.118 - 0.158: 59 0.158 - 0.197: 12 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE B 328 " pdb=" CA ILE B 328 " pdb=" CG1 ILE B 328 " pdb=" CG2 ILE B 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE D 328 " pdb=" CA ILE D 328 " pdb=" CG1 ILE D 328 " pdb=" CG2 ILE D 328 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 363 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C VAL D 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO D 364 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 363 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C VAL F 363 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 363 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO F 364 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 363 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C VAL C 363 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL C 363 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO C 364 " 0.011 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1677 3.01 - 3.48: 3262 3.48 - 3.95: 5432 3.95 - 4.43: 5280 4.43 - 4.90: 10635 Nonbonded interactions: 26286 Sorted by model distance: nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.536 2.520 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.536 2.520 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.536 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.536 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.537 2.520 ... (remaining 26281 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: 2.710 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: 12.750 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.410 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 0.065 3498 Z= 0.572 Angle : 1.336 7.165 4680 Z= 0.870 Chirality : 0.080 0.197 528 Planarity : 0.007 0.033 594 Dihedral : 12.550 66.255 1344 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 7.58 % Favored : 90.91 % 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: -3.28 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 330 PHE 0.014 0.004 PHE F 346 TYR 0.018 0.008 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.417 Fit side-chains REVERT: A 369 LYS cc_start: 0.7605 (mttt) cc_final: 0.7328 (mtpt) REVERT: B 348 ASP cc_start: 0.7680 (t0) cc_final: 0.7401 (t0) REVERT: B 349 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7693 (mmm160) REVERT: B 369 LYS cc_start: 0.7590 (mttt) cc_final: 0.7272 (mtpt) REVERT: C 348 ASP cc_start: 0.7847 (t0) cc_final: 0.7568 (t0) REVERT: C 349 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7675 (mmm160) REVERT: C 369 LYS cc_start: 0.7829 (mttt) cc_final: 0.7470 (mtpt) REVERT: D 369 LYS cc_start: 0.7939 (mttt) cc_final: 0.7633 (mtpt) REVERT: E 349 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8239 (mtp180) REVERT: E 369 LYS cc_start: 0.7754 (mttt) cc_final: 0.7428 (mtmt) REVERT: F 369 LYS cc_start: 0.7928 (mttt) cc_final: 0.7682 (mtpt) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.3335 time to fit residues: 20.4206 Evaluate side-chains 50 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS D 362 HIS E 336 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.275 Angle : 0.556 4.506 4680 Z= 0.295 Chirality : 0.050 0.134 528 Planarity : 0.004 0.032 594 Dihedral : 5.685 32.511 466 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.77 % Allowed : 9.85 % Favored : 88.38 % 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: -2.69 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.008 0.002 PHE C 378 TYR 0.009 0.004 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.355 Fit side-chains REVERT: A 369 LYS cc_start: 0.7548 (mttt) cc_final: 0.7257 (mtpt) REVERT: B 349 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7764 (mmm160) REVERT: B 369 LYS cc_start: 0.7618 (mttt) cc_final: 0.7283 (mtpt) REVERT: C 349 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7745 (mmm160) REVERT: C 369 LYS cc_start: 0.7757 (mttt) cc_final: 0.7393 (mtpt) REVERT: D 369 LYS cc_start: 0.7882 (mttt) cc_final: 0.7559 (mtmt) REVERT: E 369 LYS cc_start: 0.7679 (mttt) cc_final: 0.7393 (mtmt) REVERT: F 369 LYS cc_start: 0.8040 (mttt) cc_final: 0.7716 (mtmt) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 0.2980 time to fit residues: 18.8842 Evaluate side-chains 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.187 Angle : 0.493 4.731 4680 Z= 0.258 Chirality : 0.049 0.137 528 Planarity : 0.004 0.031 594 Dihedral : 4.776 34.609 464 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.77 % Allowed : 13.13 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.14 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.006 0.001 PHE C 378 TYR 0.015 0.003 TYR B 310 ARG 0.002 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.369 Fit side-chains REVERT: A 369 LYS cc_start: 0.7704 (mttt) cc_final: 0.7343 (mtmt) REVERT: B 349 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7784 (mmm160) REVERT: B 369 LYS cc_start: 0.7645 (mttt) cc_final: 0.7311 (mtpt) REVERT: C 349 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7768 (mmm160) REVERT: C 369 LYS cc_start: 0.7906 (mttt) cc_final: 0.7564 (mtpt) REVERT: D 369 LYS cc_start: 0.7808 (mttt) cc_final: 0.7522 (mtmt) REVERT: E 369 LYS cc_start: 0.7656 (mttt) cc_final: 0.7395 (mtmt) REVERT: F 369 LYS cc_start: 0.8045 (mttt) cc_final: 0.7730 (mtpt) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.3165 time to fit residues: 17.4226 Evaluate side-chains 48 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.248 Angle : 0.525 4.877 4680 Z= 0.276 Chirality : 0.049 0.139 528 Planarity : 0.004 0.030 594 Dihedral : 4.631 12.447 462 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.53 % Allowed : 14.39 % Favored : 83.08 % 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: -1.94 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.007 0.001 PHE C 378 TYR 0.012 0.003 TYR B 310 ARG 0.002 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.441 Fit side-chains REVERT: A 349 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8182 (mtt90) REVERT: A 369 LYS cc_start: 0.7862 (mttt) cc_final: 0.7538 (mtpt) REVERT: B 349 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7755 (mmm160) REVERT: B 369 LYS cc_start: 0.7807 (mttt) cc_final: 0.7480 (mtpt) REVERT: C 349 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7728 (mmm160) REVERT: C 369 LYS cc_start: 0.7939 (mttt) cc_final: 0.7581 (mtmt) REVERT: D 349 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7977 (mtt90) REVERT: D 369 LYS cc_start: 0.7934 (mttt) cc_final: 0.7626 (mtmt) REVERT: E 369 LYS cc_start: 0.7725 (mttt) cc_final: 0.7446 (mtmt) REVERT: F 369 LYS cc_start: 0.7999 (mttt) cc_final: 0.7727 (mtpt) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.4073 time to fit residues: 24.2083 Evaluate side-chains 55 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.300 Angle : 0.552 4.038 4680 Z= 0.290 Chirality : 0.050 0.144 528 Planarity : 0.004 0.029 594 Dihedral : 4.792 12.665 462 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 16.67 % Favored : 80.81 % 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: -1.91 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.011 0.002 PHE B 378 TYR 0.014 0.003 TYR B 310 ARG 0.006 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.439 Fit side-chains REVERT: A 349 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8153 (mtt90) REVERT: A 369 LYS cc_start: 0.7860 (mttt) cc_final: 0.7536 (mtpt) REVERT: B 349 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7677 (mmm160) REVERT: B 369 LYS cc_start: 0.7817 (mttt) cc_final: 0.7494 (mtpt) REVERT: C 349 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7763 (mmm160) REVERT: C 369 LYS cc_start: 0.8068 (mttt) cc_final: 0.7689 (mtmt) REVERT: D 369 LYS cc_start: 0.7980 (mttt) cc_final: 0.7672 (mtmt) REVERT: E 369 LYS cc_start: 0.7851 (mttt) cc_final: 0.7525 (mtmt) REVERT: F 369 LYS cc_start: 0.8028 (mttt) cc_final: 0.7751 (mtpt) REVERT: F 379 ARG cc_start: 0.3370 (ptp90) cc_final: 0.3163 (ptp90) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.3569 time to fit residues: 22.1627 Evaluate side-chains 54 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.203 Angle : 0.511 4.090 4680 Z= 0.266 Chirality : 0.049 0.141 528 Planarity : 0.003 0.027 594 Dihedral : 4.484 13.383 462 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.27 % Allowed : 19.44 % Favored : 78.28 % 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: -1.78 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.005 0.001 PHE F 346 TYR 0.012 0.003 TYR B 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.410 Fit side-chains REVERT: A 369 LYS cc_start: 0.7839 (mttt) cc_final: 0.7531 (mtpt) REVERT: B 349 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7710 (mmm160) REVERT: B 369 LYS cc_start: 0.7846 (mttt) cc_final: 0.7523 (mtpt) REVERT: C 349 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7731 (mmm160) REVERT: C 369 LYS cc_start: 0.8022 (mttt) cc_final: 0.7645 (mtmt) REVERT: C 379 ARG cc_start: 0.7036 (tpt90) cc_final: 0.6373 (tpt90) REVERT: D 369 LYS cc_start: 0.7947 (mttt) cc_final: 0.7645 (mtmt) REVERT: E 369 LYS cc_start: 0.7858 (mttt) cc_final: 0.7511 (mtpt) REVERT: F 331 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8202 (tttp) REVERT: F 369 LYS cc_start: 0.7973 (mttt) cc_final: 0.7706 (mtpt) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.3510 time to fit residues: 20.7401 Evaluate side-chains 53 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.197 Angle : 0.503 4.378 4680 Z= 0.262 Chirality : 0.049 0.140 528 Planarity : 0.003 0.029 594 Dihedral : 4.390 12.196 462 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 19.95 % Favored : 78.03 % 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: -1.63 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE B 378 TYR 0.015 0.002 TYR E 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.403 Fit side-chains REVERT: A 369 LYS cc_start: 0.7875 (mttt) cc_final: 0.7561 (mtpt) REVERT: B 349 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7736 (mmm160) REVERT: B 369 LYS cc_start: 0.7882 (mttt) cc_final: 0.7573 (mtpt) REVERT: C 349 ARG cc_start: 0.8460 (mtt180) cc_final: 0.7771 (mmm160) REVERT: C 369 LYS cc_start: 0.8042 (mttt) cc_final: 0.7680 (mtpt) REVERT: C 379 ARG cc_start: 0.6969 (tpt90) cc_final: 0.6324 (tpt90) REVERT: D 369 LYS cc_start: 0.7841 (mttt) cc_final: 0.7572 (mtmt) REVERT: E 369 LYS cc_start: 0.7877 (mttt) cc_final: 0.7539 (mtpt) REVERT: F 331 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8213 (tttp) REVERT: F 369 LYS cc_start: 0.8017 (mttt) cc_final: 0.7750 (mtpt) outliers start: 8 outliers final: 8 residues processed: 54 average time/residue: 0.3352 time to fit residues: 20.1336 Evaluate side-chains 54 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.0470 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.128 Angle : 0.475 4.967 4680 Z= 0.246 Chirality : 0.048 0.132 528 Planarity : 0.003 0.028 594 Dihedral : 4.085 11.865 462 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 19.70 % Favored : 78.28 % 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: -1.52 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.002 0.001 PHE A 378 TYR 0.017 0.002 TYR E 310 ARG 0.004 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.410 Fit side-chains REVERT: A 369 LYS cc_start: 0.7858 (mttt) cc_final: 0.7552 (mtpt) REVERT: B 349 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7717 (mmm160) REVERT: B 369 LYS cc_start: 0.7888 (mttt) cc_final: 0.7594 (mtpt) REVERT: C 349 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7768 (mmm160) REVERT: C 369 LYS cc_start: 0.8043 (mttt) cc_final: 0.7691 (mtpt) REVERT: C 379 ARG cc_start: 0.6893 (tpt90) cc_final: 0.6269 (tpt90) REVERT: D 369 LYS cc_start: 0.7805 (mttt) cc_final: 0.7552 (mtmt) REVERT: E 369 LYS cc_start: 0.7795 (mttt) cc_final: 0.7483 (mtpt) REVERT: F 331 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8188 (tttp) REVERT: F 369 LYS cc_start: 0.7962 (mttt) cc_final: 0.7691 (mtpt) outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.3122 time to fit residues: 19.0293 Evaluate side-chains 55 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3498 Z= 0.335 Angle : 0.569 5.816 4680 Z= 0.296 Chirality : 0.049 0.144 528 Planarity : 0.004 0.028 594 Dihedral : 4.778 13.044 462 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 19.44 % Favored : 78.54 % 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: -1.62 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.008 0.002 PHE F 346 TYR 0.019 0.003 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.416 Fit side-chains REVERT: A 369 LYS cc_start: 0.7950 (mttt) cc_final: 0.7644 (mtpt) REVERT: B 349 ARG cc_start: 0.8407 (mtt180) cc_final: 0.7697 (mmm160) REVERT: B 369 LYS cc_start: 0.7840 (mttt) cc_final: 0.7532 (mtpt) REVERT: C 349 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7756 (mmm160) REVERT: C 369 LYS cc_start: 0.8010 (mttt) cc_final: 0.7658 (mtpt) REVERT: C 379 ARG cc_start: 0.6872 (tpt90) cc_final: 0.6286 (tpt90) REVERT: D 369 LYS cc_start: 0.7892 (mttt) cc_final: 0.7626 (mtmt) REVERT: E 349 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8141 (mtt90) REVERT: E 369 LYS cc_start: 0.7949 (mttt) cc_final: 0.7620 (mtpt) REVERT: F 369 LYS cc_start: 0.8073 (mttt) cc_final: 0.7773 (mtpt) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.3672 time to fit residues: 22.3332 Evaluate side-chains 53 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER 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: 0.5980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.267 Angle : 0.552 6.104 4680 Z= 0.287 Chirality : 0.049 0.141 528 Planarity : 0.003 0.028 594 Dihedral : 4.713 12.592 462 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 19.70 % Favored : 78.28 % 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: -1.62 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.006 0.001 PHE F 346 TYR 0.019 0.003 TYR E 310 ARG 0.001 0.000 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7955 (mttt) cc_final: 0.7626 (mtpt) REVERT: B 349 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7678 (mmm160) REVERT: B 369 LYS cc_start: 0.7963 (mttt) cc_final: 0.7643 (mtpt) REVERT: C 349 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7736 (mmm160) REVERT: C 369 LYS cc_start: 0.8024 (mttt) cc_final: 0.7661 (mtpt) REVERT: C 379 ARG cc_start: 0.6865 (tpt90) cc_final: 0.6266 (tpt90) REVERT: D 369 LYS cc_start: 0.7868 (mttt) cc_final: 0.7618 (mtmt) REVERT: E 349 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8112 (mtt90) REVERT: E 369 LYS cc_start: 0.7873 (mttt) cc_final: 0.7550 (mtpt) REVERT: F 331 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8225 (tttp) REVERT: F 369 LYS cc_start: 0.8076 (mttt) cc_final: 0.7757 (mtpt) outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.4162 time to fit residues: 25.4365 Evaluate side-chains 56 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 overall best weight: 3.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 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 = 0.4309 r_free = 0.4309 target = 0.174683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.143132 restraints weight = 4157.634| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.14 r_work: 0.3889 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3498 Z= 0.314 Angle : 0.588 5.859 4680 Z= 0.306 Chirality : 0.050 0.143 528 Planarity : 0.004 0.026 594 Dihedral : 4.993 13.290 462 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 19.70 % Favored : 78.28 % 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: -1.77 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.007 0.001 PHE F 346 TYR 0.021 0.003 TYR E 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.43 seconds wall clock time: 26 minutes 13.47 seconds (1573.47 seconds total)