Starting phenix.real_space_refine on Thu Feb 15 01:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1h_32941/02_2024/7x1h_32941.pdb" } resolution = 2.96 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= 0.001 sd= 0.024 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 60 5.16 5 C 7084 2.51 5 N 1770 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5380 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 6 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5380 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 6 Time building chain proxies: 6.28, per 1000 atoms: 0.58 Number of scatterers: 10760 At special positions: 0 Unit cell: (100.983, 105.909, 102.625, 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 60 16.00 O 1846 8.00 N 1770 7.00 C 7084 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: 4.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 66.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.700A pdb=" N PHE A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.603A pdb=" N GLN A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.579A pdb=" N PHE A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 455 through 477 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.614A pdb=" N LEU A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 518 removed outlier: 3.501A pdb=" N GLU A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 594 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.710A pdb=" N SER A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.531A pdb=" N ILE A 615 " --> pdb=" O CYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 684 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.624A pdb=" N PHE A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.820A pdb=" N LEU A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 769 through 772 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 825 through 848 Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.581A pdb=" N ILE A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Proline residue: A 867 - end of helix removed outlier: 4.297A pdb=" N LEU A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Proline residue: A 874 - end of helix Processing helix chain 'A' and resid 878 through 887 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 147 through 160 removed outlier: 3.652A pdb=" N PHE B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.604A pdb=" N GLN B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.574A pdb=" N PHE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 401 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 435 through 453 Processing helix chain 'B' and resid 455 through 477 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.611A pdb=" N LEU B 481 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 518 Processing helix chain 'B' and resid 570 through 594 Processing helix chain 'B' and resid 595 through 597 No H-bonds generated for 'chain 'B' and resid 595 through 597' Processing helix chain 'B' and resid 601 through 611 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 654 through 684 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 696 through 713 removed outlier: 3.624A pdb=" N PHE B 713 " --> pdb=" O GLY B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.826A pdb=" N LEU B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 768 Processing helix chain 'B' and resid 769 through 772 Processing helix chain 'B' and resid 780 through 795 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 825 through 848 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 877 removed outlier: 3.572A pdb=" N ILE B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) Proline residue: B 867 - end of helix removed outlier: 4.309A pdb=" N LEU B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Proline residue: B 874 - end of helix Processing helix chain 'B' and resid 878 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143 removed outlier: 5.469A pdb=" N VAL A 235 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG A 248 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N VAL A 247 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 11.909A pdb=" N GLN A 211 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE A 249 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER A 213 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ILE A 251 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 215 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL A 253 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 217 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A 255 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N CYS A 219 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY A 200 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N SER A 213 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N ILE A 198 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N LEU A 215 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N ASP A 196 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 107 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 107 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ASP B 196 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N LEU B 215 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 11.863A pdb=" N ILE B 198 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N SER B 213 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY B 200 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 13.199A pdb=" N VAL B 247 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N GLN B 211 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N PHE B 249 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER B 213 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE B 251 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 215 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL B 253 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 217 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 255 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS B 219 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 248 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 235 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 740 removed outlier: 6.742A pdb=" N LEU A 734 " --> pdb=" O VAL A 749 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AA5, first strand: chain 'B' and resid 733 through 740 removed outlier: 6.745A pdb=" N LEU B 734 " --> pdb=" O VAL B 749 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1962 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: 4.10 Time building geometry restraints manager: 4.59 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: 2309 1.33 - 1.45: 2352 1.45 - 1.57: 6245 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 11004 Sorted by residual: bond pdb=" CA GLN A 238 " pdb=" C GLN A 238 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.20e-02 6.94e+03 1.72e+01 bond pdb=" C ILE B 251 " pdb=" O ILE B 251 " ideal model delta sigma weight residual 1.237 1.212 0.026 1.08e-02 8.57e+03 5.74e+00 bond pdb=" C ASP B 360 " pdb=" O ASP B 360 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.54e+00 bond pdb=" C ASP A 360 " pdb=" O ASP A 360 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.42e+00 bond pdb=" C PRO A 816 " pdb=" O PRO A 816 " ideal model delta sigma weight residual 1.240 1.217 0.023 1.12e-02 7.97e+03 4.25e+00 ... (remaining 10999 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.20: 330 107.20 - 113.90: 6266 113.90 - 120.60: 4660 120.60 - 127.31: 3562 127.31 - 134.01: 116 Bond angle restraints: 14934 Sorted by residual: angle pdb=" N CYS B 245 " pdb=" CA CYS B 245 " pdb=" C CYS B 245 " ideal model delta sigma weight residual 112.54 119.16 -6.62 1.22e+00 6.72e-01 2.94e+01 angle pdb=" N THR A 362 " pdb=" CA THR A 362 " pdb=" C THR A 362 " ideal model delta sigma weight residual 112.59 118.28 -5.69 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N THR B 362 " pdb=" CA THR B 362 " pdb=" C THR B 362 " ideal model delta sigma weight residual 112.26 118.22 -5.96 1.32e+00 5.74e-01 2.04e+01 angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 109.34 117.45 -8.11 2.08e+00 2.31e-01 1.52e+01 angle pdb=" N ASP B 360 " pdb=" CA ASP B 360 " pdb=" C ASP B 360 " ideal model delta sigma weight residual 111.28 107.19 4.09 1.09e+00 8.42e-01 1.41e+01 ... (remaining 14929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 5805 16.27 - 32.53: 587 32.53 - 48.80: 110 48.80 - 65.07: 16 65.07 - 81.33: 8 Dihedral angle restraints: 6526 sinusoidal: 2574 harmonic: 3952 Sorted by residual: dihedral pdb=" C PHE A 361 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " pdb=" CB PHE A 361 " ideal model delta harmonic sigma weight residual -122.60 -130.92 8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C PHE B 361 " pdb=" N PHE B 361 " pdb=" CA PHE B 361 " pdb=" CB PHE B 361 " ideal model delta harmonic sigma weight residual -122.60 -130.79 8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB LYS B 512 " pdb=" CG LYS B 512 " pdb=" CD LYS B 512 " pdb=" CE LYS B 512 " ideal model delta sinusoidal sigma weight residual -60.00 -119.60 59.60 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1564 0.065 - 0.129: 179 0.129 - 0.194: 15 0.194 - 0.259: 2 0.259 - 0.323: 4 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA PHE A 361 " pdb=" N PHE A 361 " pdb=" C PHE A 361 " pdb=" CB PHE A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PHE B 361 " pdb=" N PHE B 361 " pdb=" C PHE B 361 " pdb=" CB PHE B 361 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PHE A 354 " pdb=" N PHE A 354 " pdb=" C PHE A 354 " pdb=" CB PHE A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1761 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 213 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C SER B 213 " 0.047 2.00e-02 2.50e+03 pdb=" O SER B 213 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 214 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 774 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 775 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 774 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 775 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 775 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 775 " -0.032 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1409 2.75 - 3.29: 10665 3.29 - 3.83: 18273 3.83 - 4.36: 21592 4.36 - 4.90: 38037 Nonbonded interactions: 89976 Sorted by model distance: nonbonded pdb=" O CYS B 386 " pdb=" OG1 THR B 390 " model vdw 2.218 2.440 nonbonded pdb=" O CYS A 386 " pdb=" OG1 THR A 390 " model vdw 2.225 2.440 nonbonded pdb=" O LEU A 600 " pdb=" NH1 ARG A 605 " model vdw 2.261 2.520 nonbonded pdb=" NE2 GLN B 414 " pdb=" O LEU B 432 " model vdw 2.269 2.520 nonbonded pdb=" NE2 GLN A 414 " pdb=" O LEU A 432 " model vdw 2.271 2.520 ... (remaining 89971 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 13.900 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.850 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.050 11004 Z= 0.190 Angle : 0.564 8.498 14934 Z= 0.328 Chirality : 0.042 0.323 1764 Planarity : 0.004 0.058 1828 Dihedral : 13.096 81.334 3970 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.17 % Allowed : 0.26 % Favored : 99.57 % 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: 2.35 (0.24), residues: 1324 helix: 2.33 (0.18), residues: 848 sheet: 0.18 (0.42), residues: 108 loop : 0.20 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 515 HIS 0.003 0.001 HIS B 192 PHE 0.019 0.001 PHE A 846 TYR 0.014 0.001 TYR B 357 ARG 0.007 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 1.278 Fit side-chains REVERT: A 175 LEU cc_start: 0.7450 (mp) cc_final: 0.7189 (tt) REVERT: A 267 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6478 (pt0) REVERT: A 354 PHE cc_start: 0.8632 (t80) cc_final: 0.8406 (t80) REVERT: A 477 PHE cc_start: 0.8225 (m-80) cc_final: 0.7900 (m-10) REVERT: B 175 LEU cc_start: 0.7469 (mp) cc_final: 0.7175 (tt) REVERT: B 354 PHE cc_start: 0.8657 (t80) cc_final: 0.8415 (t80) REVERT: B 477 PHE cc_start: 0.8222 (m-80) cc_final: 0.7949 (m-10) outliers start: 2 outliers final: 1 residues processed: 270 average time/residue: 1.1661 time to fit residues: 340.2199 Evaluate side-chains 163 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 741 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN B 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 11004 Z= 0.513 Angle : 0.737 9.844 14934 Z= 0.366 Chirality : 0.048 0.189 1764 Planarity : 0.006 0.044 1828 Dihedral : 4.546 23.527 1464 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.94 % Allowed : 11.82 % Favored : 84.25 % 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: 1.15 (0.22), residues: 1324 helix: 1.47 (0.17), residues: 846 sheet: -0.07 (0.42), residues: 114 loop : -0.53 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 466 HIS 0.012 0.002 HIS B 719 PHE 0.022 0.003 PHE B 673 TYR 0.015 0.002 TYR A 638 ARG 0.006 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 1.191 Fit side-chains REVERT: A 116 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7717 (mmtt) REVERT: A 267 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6802 (pt0) REVERT: A 354 PHE cc_start: 0.8563 (t80) cc_final: 0.8335 (t80) REVERT: A 441 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: A 477 PHE cc_start: 0.8438 (m-80) cc_final: 0.8207 (m-10) REVERT: A 687 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: A 878 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 881 TYR cc_start: 0.7492 (m-10) cc_final: 0.7077 (m-80) REVERT: B 116 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7715 (mmtt) REVERT: B 267 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6851 (pt0) REVERT: B 354 PHE cc_start: 0.8573 (t80) cc_final: 0.8336 (t80) REVERT: B 441 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: B 477 PHE cc_start: 0.8342 (m-80) cc_final: 0.8083 (m-10) REVERT: B 878 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: B 881 TYR cc_start: 0.7528 (m-10) cc_final: 0.7092 (m-80) outliers start: 46 outliers final: 13 residues processed: 206 average time/residue: 1.0432 time to fit residues: 234.4264 Evaluate side-chains 157 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 884 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 684 ASN A 741 ASN B 142 ASN B 427 GLN B 684 ASN B 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11004 Z= 0.209 Angle : 0.503 5.773 14934 Z= 0.259 Chirality : 0.039 0.146 1764 Planarity : 0.004 0.041 1828 Dihedral : 4.049 20.340 1462 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.45 % Allowed : 12.93 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1324 helix: 1.69 (0.18), residues: 838 sheet: 0.35 (0.42), residues: 112 loop : -0.39 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 515 HIS 0.005 0.001 HIS B 192 PHE 0.019 0.001 PHE A 620 TYR 0.012 0.001 TYR B 441 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 1.074 Fit side-chains REVERT: A 116 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7791 (mmtt) REVERT: A 278 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6787 (t70) REVERT: A 647 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7350 (ttt) REVERT: A 687 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: A 881 TYR cc_start: 0.7439 (m-10) cc_final: 0.7052 (m-80) REVERT: B 116 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7740 (mmtt) REVERT: B 154 THR cc_start: 0.8442 (m) cc_final: 0.7993 (p) REVERT: B 266 MET cc_start: 0.7121 (mmm) cc_final: 0.6387 (tpp) REVERT: B 278 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6781 (t70) REVERT: B 441 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: B 477 PHE cc_start: 0.8339 (m-80) cc_final: 0.8117 (m-10) REVERT: B 647 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7371 (ttt) REVERT: B 662 MET cc_start: 0.7735 (ttp) cc_final: 0.7510 (ttm) REVERT: B 881 TYR cc_start: 0.7469 (m-10) cc_final: 0.7100 (m-80) outliers start: 52 outliers final: 19 residues processed: 194 average time/residue: 1.0794 time to fit residues: 228.0598 Evaluate side-chains 164 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 749 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 228 HIS A 741 ASN B 142 ASN B 228 HIS ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11004 Z= 0.320 Angle : 0.553 7.487 14934 Z= 0.280 Chirality : 0.041 0.162 1764 Planarity : 0.004 0.037 1828 Dihedral : 4.136 21.423 1462 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.28 % Allowed : 15.15 % Favored : 80.57 % 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: 1.46 (0.23), residues: 1324 helix: 1.65 (0.18), residues: 834 sheet: 0.53 (0.43), residues: 102 loop : -0.30 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 515 HIS 0.007 0.001 HIS A 719 PHE 0.018 0.002 PHE A 620 TYR 0.015 0.001 TYR B 441 ARG 0.004 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.227 Fit side-chains REVERT: A 116 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7723 (mmtt) REVERT: A 278 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6835 (t70) REVERT: A 441 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: A 633 MET cc_start: 0.8448 (mtm) cc_final: 0.8200 (mtm) REVERT: A 647 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7431 (ttt) REVERT: A 687 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: A 793 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 881 TYR cc_start: 0.7443 (m-10) cc_final: 0.7099 (m-80) REVERT: B 116 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7752 (mmtt) REVERT: B 278 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6831 (t70) REVERT: B 441 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: B 633 MET cc_start: 0.8436 (mtm) cc_final: 0.8135 (mtm) REVERT: B 647 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7443 (ttt) REVERT: B 662 MET cc_start: 0.7769 (ttp) cc_final: 0.7569 (ttm) REVERT: B 793 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8688 (mp) REVERT: B 881 TYR cc_start: 0.7481 (m-10) cc_final: 0.7231 (m-80) outliers start: 50 outliers final: 20 residues processed: 174 average time/residue: 0.9661 time to fit residues: 185.1824 Evaluate side-chains 158 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 741 ASN B 142 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11004 Z= 0.220 Angle : 0.506 8.522 14934 Z= 0.256 Chirality : 0.039 0.153 1764 Planarity : 0.004 0.040 1828 Dihedral : 3.991 20.025 1462 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.68 % Allowed : 16.35 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1324 helix: 1.73 (0.18), residues: 834 sheet: 0.81 (0.44), residues: 100 loop : -0.20 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 515 HIS 0.004 0.001 HIS B 719 PHE 0.019 0.001 PHE B 620 TYR 0.012 0.001 TYR B 441 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 1.356 Fit side-chains REVERT: A 106 VAL cc_start: 0.7826 (m) cc_final: 0.7604 (p) REVERT: A 116 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7748 (mmtt) REVERT: A 278 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6736 (t70) REVERT: A 441 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: A 687 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: A 793 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 881 TYR cc_start: 0.7446 (m-10) cc_final: 0.7042 (m-80) REVERT: B 116 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7786 (mmtt) REVERT: B 278 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6729 (t70) REVERT: B 629 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.4630 (ttt180) REVERT: B 633 MET cc_start: 0.8411 (mtm) cc_final: 0.8176 (mtm) REVERT: B 793 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 881 TYR cc_start: 0.7462 (m-10) cc_final: 0.7158 (m-80) outliers start: 43 outliers final: 20 residues processed: 161 average time/residue: 0.9690 time to fit residues: 171.7786 Evaluate side-chains 157 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 684 ASN A 741 ASN B 427 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN B 684 ASN B 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11004 Z= 0.316 Angle : 0.556 8.628 14934 Z= 0.277 Chirality : 0.041 0.163 1764 Planarity : 0.004 0.039 1828 Dihedral : 4.093 20.697 1462 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.11 % Allowed : 15.58 % Favored : 80.31 % 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: 1.41 (0.23), residues: 1324 helix: 1.61 (0.18), residues: 838 sheet: 0.72 (0.44), residues: 100 loop : -0.41 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 466 HIS 0.006 0.001 HIS B 719 PHE 0.018 0.002 PHE A 620 TYR 0.013 0.001 TYR A 441 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.282 Fit side-chains REVERT: A 106 VAL cc_start: 0.7827 (m) cc_final: 0.7601 (p) REVERT: A 116 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7769 (mmtt) REVERT: A 278 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6752 (t70) REVERT: A 441 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: A 687 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 793 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 881 TYR cc_start: 0.7474 (m-10) cc_final: 0.7102 (m-80) REVERT: B 106 VAL cc_start: 0.7855 (m) cc_final: 0.7612 (p) REVERT: B 116 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7786 (mmtt) REVERT: B 278 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6754 (t70) REVERT: B 441 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: B 629 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.4655 (ttt180) REVERT: B 633 MET cc_start: 0.8508 (mtm) cc_final: 0.8228 (mtm) REVERT: B 662 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7650 (ttm) REVERT: B 793 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 851 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7696 (mt) REVERT: B 881 TYR cc_start: 0.7511 (m-10) cc_final: 0.7246 (m-80) outliers start: 48 outliers final: 24 residues processed: 166 average time/residue: 0.9542 time to fit residues: 174.1799 Evaluate side-chains 160 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 0.0770 chunk 72 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 639 ASN A 684 ASN A 741 ASN B 427 GLN B 649 GLN B 684 ASN B 741 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11004 Z= 0.171 Angle : 0.486 9.301 14934 Z= 0.244 Chirality : 0.038 0.147 1764 Planarity : 0.004 0.041 1828 Dihedral : 3.888 18.540 1462 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.91 % Allowed : 16.95 % Favored : 80.14 % 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: 1.69 (0.23), residues: 1324 helix: 1.75 (0.18), residues: 840 sheet: 1.05 (0.48), residues: 98 loop : -0.17 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 466 HIS 0.003 0.001 HIS B 819 PHE 0.018 0.001 PHE A 620 TYR 0.011 0.001 TYR A 441 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.206 Fit side-chains REVERT: A 116 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7768 (mmtt) REVERT: A 278 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6665 (t70) REVERT: A 441 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: A 687 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: A 793 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 881 TYR cc_start: 0.7412 (m-10) cc_final: 0.7026 (m-80) REVERT: B 106 VAL cc_start: 0.7866 (m) cc_final: 0.7657 (p) REVERT: B 116 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7794 (mmtt) REVERT: B 278 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6674 (t70) REVERT: B 629 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.4575 (ttt180) REVERT: B 633 MET cc_start: 0.8408 (mtm) cc_final: 0.8183 (mtm) REVERT: B 793 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 881 TYR cc_start: 0.7433 (m-10) cc_final: 0.7120 (m-80) outliers start: 34 outliers final: 19 residues processed: 163 average time/residue: 0.9648 time to fit residues: 172.4685 Evaluate side-chains 156 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN B 427 GLN B 639 ASN B 684 ASN B 741 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11004 Z= 0.263 Angle : 0.543 9.161 14934 Z= 0.268 Chirality : 0.040 0.161 1764 Planarity : 0.004 0.042 1828 Dihedral : 3.981 19.660 1462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.00 % Allowed : 17.64 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1324 helix: 1.63 (0.18), residues: 846 sheet: 1.07 (0.48), residues: 98 loop : -0.34 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 466 HIS 0.006 0.001 HIS B 719 PHE 0.019 0.001 PHE B 620 TYR 0.012 0.001 TYR A 441 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.293 Fit side-chains REVERT: A 116 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7786 (mmtt) REVERT: A 278 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6735 (t70) REVERT: A 441 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 687 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: A 793 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 881 TYR cc_start: 0.7443 (m-10) cc_final: 0.7056 (m-80) REVERT: B 106 VAL cc_start: 0.7848 (m) cc_final: 0.7629 (p) REVERT: B 116 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7810 (mmtt) REVERT: B 278 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6719 (t70) REVERT: B 441 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: B 629 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.4625 (ttt180) REVERT: B 633 MET cc_start: 0.8495 (mtm) cc_final: 0.8252 (mtm) REVERT: B 793 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 881 TYR cc_start: 0.7448 (m-10) cc_final: 0.7134 (m-80) outliers start: 35 outliers final: 21 residues processed: 164 average time/residue: 0.9986 time to fit residues: 179.4847 Evaluate side-chains 157 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 876 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 0.0770 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 741 ASN B 427 GLN B 639 ASN B 649 GLN B 684 ASN B 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11004 Z= 0.156 Angle : 0.492 9.681 14934 Z= 0.245 Chirality : 0.038 0.146 1764 Planarity : 0.004 0.042 1828 Dihedral : 3.794 16.932 1462 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 18.15 % Favored : 79.45 % 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: 1.75 (0.23), residues: 1324 helix: 1.78 (0.18), residues: 842 sheet: 0.88 (0.48), residues: 110 loop : -0.09 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.003 0.001 HIS B 192 PHE 0.017 0.001 PHE B 620 TYR 0.011 0.001 TYR A 441 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.176 Fit side-chains REVERT: A 116 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7771 (mmtt) REVERT: A 687 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: B 116 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7794 (mmtt) REVERT: B 793 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 881 TYR cc_start: 0.7456 (m-10) cc_final: 0.7138 (m-80) outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 0.9287 time to fit residues: 168.3106 Evaluate side-chains 151 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 876 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 113 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN B 427 GLN B 639 ASN B 684 ASN B 741 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11004 Z= 0.238 Angle : 0.533 9.561 14934 Z= 0.263 Chirality : 0.040 0.161 1764 Planarity : 0.004 0.042 1828 Dihedral : 3.888 18.664 1462 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.05 % Allowed : 18.24 % Favored : 79.71 % 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: 1.75 (0.23), residues: 1324 helix: 1.79 (0.18), residues: 834 sheet: 1.22 (0.49), residues: 98 loop : -0.17 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 466 HIS 0.006 0.001 HIS A 719 PHE 0.018 0.001 PHE B 620 TYR 0.011 0.001 TYR A 441 ARG 0.002 0.000 ARG B 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.234 Fit side-chains REVERT: A 116 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7744 (mmtt) REVERT: A 687 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: B 116 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7839 (mmpt) REVERT: B 793 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 881 TYR cc_start: 0.7500 (m-10) cc_final: 0.7167 (m-80) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.9599 time to fit residues: 159.9208 Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 MET Chi-restraints excluded: chain B residue 876 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 741 ASN B 639 ASN B 649 GLN B 741 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117310 restraints weight = 12118.454| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.60 r_work: 0.3210 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11004 Z= 0.204 Angle : 0.512 9.790 14934 Z= 0.255 Chirality : 0.039 0.155 1764 Planarity : 0.004 0.043 1828 Dihedral : 3.859 18.404 1462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 18.84 % Favored : 79.20 % 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: 1.66 (0.23), residues: 1324 helix: 1.73 (0.18), residues: 846 sheet: 0.88 (0.47), residues: 110 loop : -0.22 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 466 HIS 0.004 0.001 HIS A 719 PHE 0.017 0.001 PHE A 620 TYR 0.012 0.001 TYR A 441 ARG 0.002 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.48 seconds wall clock time: 74 minutes 21.96 seconds (4461.96 seconds total)