Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:45:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7p_18228/10_2023/8q7p_18228.pdb" } resolution = 3.28 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= 0.003 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 2136 2.51 5 N 618 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3402 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.22, per 1000 atoms: 0.65 Number of scatterers: 3402 At special positions: 0 Unit cell: (122.136, 102.507, 38.531, 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 618 7.00 C 2136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 489.7 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: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 50.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.845A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.738A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 333 through 334 removed outlier: 6.877A pdb=" N GLY B 333 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.572A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.626A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.626A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 357 through 358 removed outlier: 7.115A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.404A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.458A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB4, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.857A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.279A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.459A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.830A pdb=" N GLY A 333 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.535A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.626A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 358 removed outlier: 7.093A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.367A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 377 removed outlier: 6.459A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 276 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: 0.81 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1042 1.34 - 1.46: 387 1.46 - 1.58: 2021 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3456 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.51e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.44e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.26e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.19e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 101.30 - 106.94: 190 106.94 - 112.57: 1649 112.57 - 118.21: 883 118.21 - 123.84: 1607 123.84 - 129.48: 297 Bond angle restraints: 4626 Sorted by residual: angle pdb=" OE1 GLN E 336 " pdb=" CD GLN E 336 " pdb=" NE2 GLN E 336 " ideal model delta sigma weight residual 122.60 117.65 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.66 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA LYS D 331 " pdb=" C LYS D 331 " pdb=" N PRO D 332 " ideal model delta sigma weight residual 118.16 121.60 -3.44 7.00e-01 2.04e+00 2.41e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 117.75 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" N SER E 356 " pdb=" CA SER E 356 " pdb=" C SER E 356 " ideal model delta sigma weight residual 111.36 116.63 -5.27 1.09e+00 8.42e-01 2.34e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 1959 14.57 - 29.14: 97 29.14 - 43.71: 22 43.71 - 58.28: 6 58.28 - 72.85: 10 Dihedral angle restraints: 2094 sinusoidal: 864 harmonic: 1230 Sorted by residual: dihedral pdb=" CA ASN B 327 " pdb=" C ASN B 327 " pdb=" N ILE B 328 " pdb=" CA ILE B 328 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 371 " pdb=" C ILE B 371 " pdb=" N GLU B 372 " pdb=" CA GLU B 372 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C LYS E 347 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 279 0.062 - 0.123: 164 0.123 - 0.185: 53 0.185 - 0.247: 15 0.247 - 0.308: 11 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA GLU B 342 " pdb=" N GLU B 342 " pdb=" C GLU B 342 " pdb=" CB GLU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU A 342 " pdb=" N GLU A 342 " pdb=" C GLU A 342 " pdb=" CB GLU A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.066 2.00e-02 2.50e+03 3.37e-02 2.27e+01 pdb=" CG TYR F 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.066 2.00e-02 2.50e+03 3.35e-02 2.24e+01 pdb=" CG TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " 0.044 2.00e-02 2.50e+03 3.31e-02 1.64e+01 pdb=" CG HIS D 362 " -0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " 0.026 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1408 2.96 - 3.45: 2645 3.45 - 3.93: 5364 3.93 - 4.42: 5382 4.42 - 4.90: 10371 Nonbonded interactions: 25170 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.479 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.488 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.502 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.546 2.440 ... (remaining 25165 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.420 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.011 0.036 3456 Z= 0.723 Angle : 1.825 6.739 4626 Z= 1.232 Chirality : 0.091 0.308 522 Planarity : 0.009 0.035 588 Dihedral : 11.615 72.854 1314 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 438 *********************** 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 142 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2316 time to fit residues: 37.2416 Evaluate side-chains 80 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN C 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3456 Z= 0.240 Angle : 0.613 4.740 4626 Z= 0.321 Chirality : 0.053 0.153 522 Planarity : 0.004 0.029 588 Dihedral : 5.779 17.098 456 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.54 % Allowed : 10.51 % Favored : 87.95 % 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: -1.36 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 438 *********************** 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 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.423 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.1253 time to fit residues: 14.1557 Evaluate side-chains 76 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.184 Angle : 0.566 7.525 4626 Z= 0.282 Chirality : 0.052 0.163 522 Planarity : 0.003 0.024 588 Dihedral : 5.148 16.141 456 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.28 % Allowed : 13.59 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.42 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 438 *********************** 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 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.400 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.1002 time to fit residues: 10.8192 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0396 time to fit residues: 0.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS A 329 HIS A 336 GLN C 336 GLN C 368 ASN E 336 GLN E 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 3456 Z= 0.652 Angle : 0.788 6.269 4626 Z= 0.407 Chirality : 0.055 0.174 522 Planarity : 0.004 0.022 588 Dihedral : 6.273 19.132 456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.79 % Allowed : 14.87 % Favored : 83.33 % 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: -1.95 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 438 *********************** 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 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.484 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.1137 time to fit residues: 12.4468 Evaluate side-chains 75 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0341 time to fit residues: 0.8913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.024 3456 Z= 0.148 Angle : 0.559 7.133 4626 Z= 0.279 Chirality : 0.050 0.162 522 Planarity : 0.002 0.021 588 Dihedral : 5.190 15.045 456 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 17.95 % Favored : 82.05 % 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: -1.83 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 438 *********************** 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 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.427 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0884 time to fit residues: 10.0173 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.230 Angle : 0.559 5.828 4626 Z= 0.278 Chirality : 0.050 0.132 522 Planarity : 0.002 0.017 588 Dihedral : 5.033 16.660 456 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.03 % Allowed : 16.92 % Favored : 82.05 % 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: -1.90 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 *********************** 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 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.379 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 74 average time/residue: 0.0832 time to fit residues: 8.6605 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0326 time to fit residues: 0.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 0.0470 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3456 Z= 0.288 Angle : 0.598 8.115 4626 Z= 0.297 Chirality : 0.051 0.177 522 Planarity : 0.003 0.017 588 Dihedral : 5.171 15.743 456 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.51 % Allowed : 18.46 % Favored : 81.03 % 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: -2.02 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.26), residues: 438 *********************** 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 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.438 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.0891 time to fit residues: 8.9068 Evaluate side-chains 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0473 time to fit residues: 0.7021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3456 Z= 0.301 Angle : 0.601 6.601 4626 Z= 0.297 Chirality : 0.051 0.195 522 Planarity : 0.002 0.017 588 Dihedral : 5.187 16.955 456 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.77 % Allowed : 18.97 % Favored : 80.26 % 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: -2.10 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.26), residues: 438 *********************** 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 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.395 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 0.0892 time to fit residues: 8.9202 Evaluate side-chains 72 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0335 time to fit residues: 0.7610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.194 Angle : 0.550 7.619 4626 Z= 0.270 Chirality : 0.050 0.174 522 Planarity : 0.002 0.016 588 Dihedral : 4.869 15.585 456 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 19.74 % Favored : 80.26 % 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: -2.08 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.26), residues: 438 *********************** 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 70 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.400 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0896 time to fit residues: 8.7788 Evaluate side-chains 69 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3456 Z= 0.107 Angle : 0.511 7.763 4626 Z= 0.246 Chirality : 0.050 0.152 522 Planarity : 0.002 0.018 588 Dihedral : 4.433 12.812 456 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.26 % Allowed : 20.26 % Favored : 79.49 % 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: -2.09 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 438 ********************** 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 72 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.411 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.0890 time to fit residues: 8.8718 Evaluate side-chains 70 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126863 restraints weight = 5113.992| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.24 r_work: 0.3810 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3456 Z= 0.373 Angle : 0.631 6.625 4626 Z= 0.312 Chirality : 0.052 0.188 522 Planarity : 0.003 0.016 588 Dihedral : 5.141 17.441 456 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 19.23 % Favored : 79.49 % 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: -2.12 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.60 seconds wall clock time: 22 minutes 52.60 seconds (1372.60 seconds total)