Starting phenix.real_space_refine on Thu Dec 7 18:25:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjy_14026/12_2023/7qjy_14026.pdb" } resolution = 3.14 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= 0.004 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 ARG 349": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.41, per 1000 atoms: 0.70 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.1, 132.98, 45.78, 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: 1.18 Conformation dependent library (CDL) restraints added in 627.8 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 16 sheets defined 0.0% alpha, 48.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.853A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.733A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.594A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.621A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354 removed outlier: 9.075A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N LEU D 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 removed outlier: 6.435A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.820A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.014A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER E 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY C 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LYS F 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY F 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS C 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER C 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.573A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.234A pdb=" N VAL C 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.748A pdb=" N LEU C 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.525A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 216 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: 0.76 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 988 1.33 - 1.45: 430 1.45 - 1.57: 2074 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.08e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" C GLY D 323 " pdb=" O GLY D 323 " ideal model delta sigma weight residual 1.236 1.222 0.014 5.30e-03 3.56e+04 6.52e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.33e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.20e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 101.50 - 107.13: 194 107.13 - 112.77: 1686 112.77 - 118.40: 883 118.40 - 124.03: 1639 124.03 - 129.67: 278 Bond angle restraints: 4680 Sorted by residual: angle pdb=" OD1 ASN D 327 " pdb=" CG ASN D 327 " pdb=" ND2 ASN D 327 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" N GLY A 367 " pdb=" CA GLY A 367 " pdb=" C GLY A 367 " ideal model delta sigma weight residual 114.61 121.51 -6.90 1.49e+00 4.50e-01 2.14e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.56 128.34 -6.78 1.56e+00 4.11e-01 1.89e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.05 127.23 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" OD1 ASN A 327 " pdb=" CG ASN A 327 " pdb=" ND2 ASN A 327 " ideal model delta sigma weight residual 122.60 118.30 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 1967 16.44 - 32.88: 143 32.88 - 49.32: 18 49.32 - 65.75: 3 65.75 - 82.19: 5 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 366 " pdb=" C GLY B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLY A 366 " pdb=" C GLY A 366 " pdb=" N GLY A 367 " pdb=" CA GLY A 367 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLY D 366 " pdb=" C GLY D 366 " pdb=" N GLY D 367 " pdb=" CA GLY D 367 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 314 0.070 - 0.140: 174 0.140 - 0.211: 33 0.211 - 0.281: 4 0.281 - 0.351: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS C 329 " pdb=" N HIS C 329 " pdb=" C HIS C 329 " pdb=" CB HIS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA HIS D 329 " pdb=" N HIS D 329 " pdb=" C HIS D 329 " pdb=" CB HIS D 329 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA HIS A 329 " pdb=" N HIS A 329 " pdb=" C HIS A 329 " pdb=" CB HIS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.139 2.00e-02 2.50e+03 7.57e-02 1.15e+02 pdb=" CG TYR F 310 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.115 2.00e-02 2.50e+03 6.66e-02 8.88e+01 pdb=" CG TYR D 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.106 2.00e-02 2.50e+03 6.04e-02 7.29e+01 pdb=" CG TYR C 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.100 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1660 3.00 - 3.47: 2701 3.47 - 3.95: 5423 3.95 - 4.42: 5462 4.42 - 4.90: 10569 Nonbonded interactions: 25815 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.525 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.536 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.543 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.548 2.440 ... (remaining 25810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 3.630 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.820 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.039 3498 Z= 0.740 Angle : 1.870 8.465 4680 Z= 1.233 Chirality : 0.085 0.351 528 Planarity : 0.013 0.095 594 Dihedral : 12.320 82.193 1344 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.25 % Allowed : 2.53 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.005 HIS F 330 PHE 0.055 0.013 PHE F 346 TYR 0.139 0.043 TYR F 310 ARG 0.004 0.001 ARG B 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 156 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.426 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.3016 time to fit residues: 51.6777 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5793 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 374 HIS C 359 ASN C 374 HIS D 307 GLN D 374 HIS E 327 ASN E 329 HIS E 359 ASN F 374 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.258 Angle : 0.719 7.440 4680 Z= 0.367 Chirality : 0.050 0.132 528 Planarity : 0.005 0.048 594 Dihedral : 6.409 22.256 462 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % Favored : 84.85 % 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: -2.41 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.012 0.003 PHE C 346 TYR 0.016 0.004 TYR F 310 ARG 0.008 0.001 ARG C 349 *********************** 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 116 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.425 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.3029 time to fit residues: 37.3934 Evaluate side-chains 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0409 time to fit residues: 0.8762 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 359 ASN A 374 HIS B 329 HIS E 327 ASN E 359 ASN E 374 HIS F 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 3498 Z= 0.528 Angle : 0.793 8.654 4680 Z= 0.404 Chirality : 0.051 0.163 528 Planarity : 0.005 0.052 594 Dihedral : 6.413 24.895 462 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 14.39 % Favored : 83.59 % 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: -2.32 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 374 PHE 0.015 0.003 PHE C 346 TYR 0.021 0.005 TYR F 310 ARG 0.005 0.001 ARG C 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 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.2629 time to fit residues: 25.7412 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1190 time to fit residues: 1.3325 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4994 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= 0.279 Angle : 0.634 7.282 4680 Z= 0.317 Chirality : 0.048 0.129 528 Planarity : 0.005 0.050 594 Dihedral : 5.834 22.061 462 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 16.67 % Favored : 81.31 % 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: -2.18 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.009 0.002 PHE C 346 TYR 0.017 0.003 TYR A 310 ARG 0.007 0.001 ARG C 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 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.450 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.2648 time to fit residues: 25.7573 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0375 time to fit residues: 0.8200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 327 ASN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3498 Z= 0.328 Angle : 0.647 7.127 4680 Z= 0.324 Chirality : 0.048 0.127 528 Planarity : 0.005 0.049 594 Dihedral : 5.726 22.003 462 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 16.92 % Favored : 81.57 % 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: -2.19 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.010 0.002 PHE C 346 TYR 0.019 0.004 TYR A 310 ARG 0.006 0.001 ARG C 349 *********************** 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 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.417 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.2483 time to fit residues: 24.8258 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.7427 ------------------------------------------------------------------------------- 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: 8.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 0.0570 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS D 336 GLN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5298 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= 0.280 Angle : 0.614 6.887 4680 Z= 0.309 Chirality : 0.047 0.127 528 Planarity : 0.004 0.048 594 Dihedral : 5.537 20.919 462 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 16.92 % 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: -2.15 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.009 0.002 PHE C 346 TYR 0.018 0.003 TYR A 310 ARG 0.003 0.001 ARG C 349 *********************** 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 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.415 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 0.2464 time to fit residues: 23.3676 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0338 time to fit residues: 0.8226 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 327 ASN F 359 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 3498 Z= 0.553 Angle : 0.766 7.871 4680 Z= 0.389 Chirality : 0.050 0.140 528 Planarity : 0.005 0.047 594 Dihedral : 6.138 24.648 462 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % 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: -2.42 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 330 PHE 0.016 0.003 PHE C 346 TYR 0.020 0.005 TYR F 310 ARG 0.005 0.001 ARG C 349 *********************** 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 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.424 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.2618 time to fit residues: 22.0509 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0351 time to fit residues: 0.7178 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3498 Z= 0.246 Angle : 0.619 6.295 4680 Z= 0.314 Chirality : 0.047 0.140 528 Planarity : 0.004 0.049 594 Dihedral : 5.617 21.121 462 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.51 % Allowed : 19.70 % Favored : 79.80 % 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: -2.24 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.007 0.002 PHE C 346 TYR 0.019 0.003 TYR A 310 ARG 0.004 0.000 ARG C 349 *********************** 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 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.492 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.2416 time to fit residues: 22.4807 Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6172 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.143 Angle : 0.552 5.593 4680 Z= 0.278 Chirality : 0.047 0.137 528 Planarity : 0.005 0.050 594 Dihedral : 4.895 17.104 462 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.51 % Allowed : 19.70 % Favored : 79.80 % 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 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.006 0.001 PHE A 378 TYR 0.017 0.003 TYR A 310 ARG 0.007 0.001 ARG C 349 *********************** 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 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.421 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.2350 time to fit residues: 21.1690 Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0373 time to fit residues: 0.6494 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS D 327 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3498 Z= 0.240 Angle : 0.610 6.781 4680 Z= 0.303 Chirality : 0.047 0.129 528 Planarity : 0.005 0.046 594 Dihedral : 5.141 18.856 462 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.25 % Allowed : 20.45 % Favored : 79.29 % 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: -2.04 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.008 0.002 PHE D 378 TYR 0.019 0.003 TYR A 310 ARG 0.008 0.001 ARG C 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 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.459 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2189 time to fit residues: 18.7951 Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6097 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.121604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112777 restraints weight = 5034.854| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.66 r_work: 0.3532 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3498 Z= 0.435 Angle : 0.715 7.213 4680 Z= 0.361 Chirality : 0.049 0.135 528 Planarity : 0.005 0.044 594 Dihedral : 5.772 22.284 462 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.76 % Allowed : 20.45 % Favored : 78.79 % 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: -2.24 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.013 0.003 PHE C 346 TYR 0.020 0.004 TYR A 310 ARG 0.005 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.52 seconds wall clock time: 23 minutes 47.94 seconds (1427.94 seconds total)