Starting phenix.real_space_refine on Thu Feb 15 01:31:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1g_32940/02_2024/7x1g_32940.pdb" } resolution = 2.94 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= 0.026 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: 5.98, per 1000 atoms: 0.56 Number of scatterers: 10760 At special positions: 0 Unit cell: (122.329, 87.847, 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 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 66.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.701A pdb=" N PHE A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.967A 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 362 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: 3.964A 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 362 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: 3.612A 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: 4.310A 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: 6.496A 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: 11.908A 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: 6.739A 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: 11.850A pdb=" N ILE A 198 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LEU A 215 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 10.948A 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: 10.951A pdb=" N ASP B 196 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N LEU B 215 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N ILE B 198 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 9.041A 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: 13.180A pdb=" N VAL B 247 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N GLN B 211 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N PHE B 249 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER B 213 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 251 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 215 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 253 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 217 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 8.082A 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: 6.453A 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: 6.746A 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: 3.71 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1633 1.31 - 1.43: 2986 1.43 - 1.56: 6287 1.56 - 1.68: 0 1.68 - 1.81: 98 Bond restraints: 11004 Sorted by residual: bond pdb=" CA TRP B 240 " pdb=" C TRP B 240 " ideal model delta sigma weight residual 1.525 1.477 0.047 1.11e-02 8.12e+03 1.82e+01 bond pdb=" C ASN B 239 " pdb=" O ASN B 239 " ideal model delta sigma weight residual 1.234 1.185 0.049 1.19e-02 7.06e+03 1.70e+01 bond pdb=" CA GLU B 242 " pdb=" C GLU B 242 " ideal model delta sigma weight residual 1.519 1.469 0.050 1.22e-02 6.72e+03 1.70e+01 bond pdb=" C TYR B 357 " pdb=" N PRO B 358 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.36e-02 5.41e+03 1.13e+01 bond pdb=" C TYR A 357 " pdb=" N PRO A 358 " ideal model delta sigma weight residual 1.335 1.381 -0.045 1.36e-02 5.41e+03 1.11e+01 ... (remaining 10999 not shown) Histogram of bond angle deviations from ideal: 100.51 - 108.18: 421 108.18 - 115.85: 6754 115.85 - 123.51: 7509 123.51 - 131.18: 215 131.18 - 138.85: 35 Bond angle restraints: 14934 Sorted by residual: angle pdb=" N TRP B 240 " pdb=" CA TRP B 240 " pdb=" C TRP B 240 " ideal model delta sigma weight residual 113.50 103.04 10.46 1.65e+00 3.67e-01 4.02e+01 angle pdb=" C TYR A 357 " pdb=" N PRO A 358 " pdb=" CA PRO A 358 " ideal model delta sigma weight residual 119.05 112.38 6.67 1.11e+00 8.12e-01 3.61e+01 angle pdb=" C TYR B 357 " pdb=" N PRO B 358 " pdb=" CA PRO B 358 " ideal model delta sigma weight residual 119.05 112.43 6.62 1.11e+00 8.12e-01 3.56e+01 angle pdb=" N GLU B 242 " pdb=" CA GLU B 242 " pdb=" C GLU B 242 " ideal model delta sigma weight residual 113.55 107.02 6.53 1.26e+00 6.30e-01 2.69e+01 angle pdb=" N ASN B 243 " pdb=" CA ASN B 243 " pdb=" C ASN B 243 " ideal model delta sigma weight residual 111.87 104.96 6.91 1.41e+00 5.03e-01 2.40e+01 ... (remaining 14929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 5806 16.27 - 32.54: 581 32.54 - 48.80: 116 48.80 - 65.07: 15 65.07 - 81.34: 8 Dihedral angle restraints: 6526 sinusoidal: 2574 harmonic: 3952 Sorted by residual: 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 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 512 " pdb=" CG LYS A 512 " pdb=" CD LYS A 512 " pdb=" CE LYS A 512 " ideal model delta sinusoidal sigma weight residual -60.00 -119.53 59.53 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASN B 239 " pdb=" C ASN B 239 " pdb=" CA ASN B 239 " pdb=" CB ASN B 239 " ideal model delta harmonic sigma weight residual 122.80 115.21 7.59 0 2.50e+00 1.60e-01 9.22e+00 ... (remaining 6523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1440 0.044 - 0.087: 243 0.087 - 0.131: 75 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ARG A 822 " pdb=" N ARG A 822 " pdb=" C ARG A 822 " pdb=" CB ARG A 822 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 239 " pdb=" N ASN B 239 " pdb=" C ASN B 239 " pdb=" CB ASN B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA GLU A 242 " pdb=" N GLU A 242 " pdb=" C GLU A 242 " pdb=" CB GLU A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1761 not shown) Planarity restraints: 1828 Sorted by residual: 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 5.69e-02 5.17e+00 pdb=" N PRO A 775 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 775 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 775 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 239 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" CG ASN B 239 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 239 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 239 " 0.009 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1403 2.75 - 3.29: 10666 3.29 - 3.83: 18274 3.83 - 4.36: 21620 4.36 - 4.90: 37999 Nonbonded interactions: 89962 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=" OH TYR B 357 " pdb=" O LEU B 423 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR A 357 " pdb=" O LEU A 423 " model vdw 2.237 2.440 nonbonded pdb=" O LEU A 600 " pdb=" NH1 ARG A 605 " model vdw 2.261 2.520 ... (remaining 89957 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.560 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 31.180 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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= 0.195 Angle : 0.554 13.851 14934 Z= 0.314 Chirality : 0.038 0.219 1764 Planarity : 0.003 0.058 1828 Dihedral : 13.159 81.339 3970 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % 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: 2.38 (0.24), residues: 1324 helix: 2.30 (0.18), residues: 862 sheet: -0.00 (0.41), residues: 108 loop : 0.37 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 240 HIS 0.003 0.001 HIS B 192 PHE 0.019 0.001 PHE A 846 TYR 0.006 0.001 TYR B 357 ARG 0.006 0.000 ARG A 823 *********************** 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 250 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 1.264 Fit side-chains REVERT: A 596 LYS cc_start: 0.8402 (mttt) cc_final: 0.8099 (mtpt) REVERT: A 734 LEU cc_start: 0.7972 (mt) cc_final: 0.7679 (mp) REVERT: B 106 VAL cc_start: 0.8196 (m) cc_final: 0.7909 (p) REVERT: B 596 LYS cc_start: 0.8383 (mttt) cc_final: 0.8061 (mtpt) REVERT: B 734 LEU cc_start: 0.7978 (mt) cc_final: 0.7664 (mp) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 1.1669 time to fit residues: 314.8931 Evaluate side-chains 149 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 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: 1.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN A 467 ASN A 741 ASN B 239 ASN B 443 GLN B 467 ASN B 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11004 Z= 0.370 Angle : 0.592 7.939 14934 Z= 0.301 Chirality : 0.043 0.163 1764 Planarity : 0.005 0.034 1828 Dihedral : 4.016 18.960 1464 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.00 % Allowed : 10.02 % Favored : 86.99 % 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: 1.92 (0.23), residues: 1324 helix: 2.06 (0.18), residues: 844 sheet: 0.38 (0.43), residues: 108 loop : -0.24 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 515 HIS 0.008 0.002 HIS B 719 PHE 0.019 0.002 PHE A 636 TYR 0.021 0.002 TYR A 441 ARG 0.005 0.000 ARG A 157 *********************** 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 186 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.269 Fit side-chains REVERT: A 479 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 596 LYS cc_start: 0.8494 (mttt) cc_final: 0.8121 (mtpt) REVERT: A 809 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 596 LYS cc_start: 0.8467 (mttt) cc_final: 0.8079 (mtpt) REVERT: B 809 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8086 (mt) outliers start: 35 outliers final: 12 residues processed: 174 average time/residue: 1.1973 time to fit residues: 225.4100 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11004 Z= 0.272 Angle : 0.527 5.959 14934 Z= 0.267 Chirality : 0.041 0.153 1764 Planarity : 0.004 0.042 1828 Dihedral : 3.981 19.363 1462 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.77 % Allowed : 11.99 % 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: 1.81 (0.23), residues: 1324 helix: 1.97 (0.18), residues: 844 sheet: 0.48 (0.43), residues: 108 loop : -0.31 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 515 HIS 0.006 0.001 HIS A 719 PHE 0.016 0.002 PHE A 620 TYR 0.015 0.001 TYR A 441 ARG 0.006 0.000 ARG B 347 *********************** 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 185 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.211 Fit side-chains REVERT: A 596 LYS cc_start: 0.8490 (mttt) cc_final: 0.8112 (mtpt) REVERT: B 596 LYS cc_start: 0.8472 (mttt) cc_final: 0.8078 (mtpt) REVERT: B 809 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8088 (mt) outliers start: 44 outliers final: 17 residues processed: 167 average time/residue: 1.1317 time to fit residues: 205.3336 Evaluate side-chains 150 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN B 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11004 Z= 0.422 Angle : 0.602 6.676 14934 Z= 0.303 Chirality : 0.044 0.166 1764 Planarity : 0.005 0.048 1828 Dihedral : 4.252 21.708 1462 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.79 % Allowed : 13.01 % Favored : 82.19 % 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: 1.40 (0.23), residues: 1324 helix: 1.67 (0.18), residues: 852 sheet: 0.24 (0.42), residues: 114 loop : -0.56 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 515 HIS 0.008 0.002 HIS A 719 PHE 0.018 0.002 PHE A 636 TYR 0.021 0.002 TYR A 441 ARG 0.007 0.001 ARG B 347 *********************** 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 203 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 1.093 Fit side-chains REVERT: A 363 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: A 479 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 508 LYS cc_start: 0.7670 (mttt) cc_final: 0.7444 (mttp) REVERT: A 596 LYS cc_start: 0.8524 (mttt) cc_final: 0.8078 (mtpt) REVERT: A 797 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 363 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: B 479 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 508 LYS cc_start: 0.7679 (mttt) cc_final: 0.7464 (mttp) REVERT: B 596 LYS cc_start: 0.8494 (mttt) cc_final: 0.8086 (mtpt) REVERT: B 809 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (mt) outliers start: 56 outliers final: 22 residues processed: 181 average time/residue: 1.1280 time to fit residues: 221.9481 Evaluate side-chains 165 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 0.0070 chunk 53 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11004 Z= 0.178 Angle : 0.490 6.608 14934 Z= 0.249 Chirality : 0.039 0.152 1764 Planarity : 0.004 0.046 1828 Dihedral : 3.974 19.726 1462 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.00 % Allowed : 15.41 % Favored : 81.59 % 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: 1.74 (0.23), residues: 1324 helix: 1.96 (0.18), residues: 844 sheet: 0.30 (0.43), residues: 114 loop : -0.41 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.005 0.001 HIS B 192 PHE 0.017 0.001 PHE B 620 TYR 0.014 0.001 TYR A 441 ARG 0.006 0.000 ARG B 157 *********************** 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 181 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.159 Fit side-chains REVERT: A 370 LYS cc_start: 0.7508 (mmtp) cc_final: 0.7218 (mmtm) REVERT: A 479 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 596 LYS cc_start: 0.8505 (mttt) cc_final: 0.8091 (mtpt) REVERT: B 106 VAL cc_start: 0.8420 (m) cc_final: 0.8118 (p) REVERT: B 370 LYS cc_start: 0.7504 (mmtp) cc_final: 0.7210 (mmtm) REVERT: B 479 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8227 (mp) REVERT: B 596 LYS cc_start: 0.8473 (mttt) cc_final: 0.8046 (mtpt) outliers start: 35 outliers final: 14 residues processed: 168 average time/residue: 1.1769 time to fit residues: 214.7525 Evaluate side-chains 155 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11004 Z= 0.390 Angle : 0.574 6.891 14934 Z= 0.289 Chirality : 0.043 0.164 1764 Planarity : 0.005 0.049 1828 Dihedral : 4.185 20.942 1462 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.85 % Allowed : 15.50 % Favored : 80.65 % 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: 1.55 (0.23), residues: 1324 helix: 1.82 (0.18), residues: 840 sheet: 0.27 (0.43), residues: 114 loop : -0.50 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 515 HIS 0.008 0.002 HIS B 719 PHE 0.017 0.002 PHE B 620 TYR 0.019 0.002 TYR A 441 ARG 0.005 0.000 ARG A 157 *********************** 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 194 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.209 Fit side-chains REVERT: A 363 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: A 370 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7392 (mmtm) REVERT: A 479 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 596 LYS cc_start: 0.8484 (mttt) cc_final: 0.8115 (mtpt) REVERT: A 741 ASN cc_start: 0.7953 (t0) cc_final: 0.7728 (t0) REVERT: A 809 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8181 (mt) REVERT: B 363 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: B 370 LYS cc_start: 0.7659 (mmtp) cc_final: 0.7389 (mmtm) REVERT: B 479 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 596 LYS cc_start: 0.8454 (mttt) cc_final: 0.8075 (mtpt) REVERT: B 741 ASN cc_start: 0.7951 (t0) cc_final: 0.7733 (t0) outliers start: 45 outliers final: 23 residues processed: 178 average time/residue: 1.1162 time to fit residues: 215.7087 Evaluate side-chains 163 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 749 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11004 Z= 0.223 Angle : 0.506 6.898 14934 Z= 0.256 Chirality : 0.040 0.157 1764 Planarity : 0.004 0.048 1828 Dihedral : 4.039 19.859 1462 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.42 % Allowed : 16.27 % 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: 1.74 (0.23), residues: 1324 helix: 1.99 (0.18), residues: 832 sheet: 0.30 (0.43), residues: 112 loop : -0.41 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 515 HIS 0.005 0.001 HIS B 192 PHE 0.016 0.001 PHE A 620 TYR 0.016 0.001 TYR B 441 ARG 0.009 0.000 ARG B 347 *********************** 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 181 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 0.986 Fit side-chains REVERT: A 363 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: A 479 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 596 LYS cc_start: 0.8458 (mttt) cc_final: 0.8124 (mtpt) REVERT: A 809 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 363 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: B 479 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 596 LYS cc_start: 0.8429 (mttt) cc_final: 0.8079 (mtpt) outliers start: 40 outliers final: 18 residues processed: 165 average time/residue: 1.0846 time to fit residues: 194.0988 Evaluate side-chains 161 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11004 Z= 0.262 Angle : 0.518 7.043 14934 Z= 0.262 Chirality : 0.040 0.157 1764 Planarity : 0.004 0.048 1828 Dihedral : 4.055 19.861 1462 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.91 % Allowed : 16.87 % Favored : 80.22 % 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: 1.75 (0.23), residues: 1324 helix: 1.97 (0.18), residues: 832 sheet: 0.38 (0.44), residues: 112 loop : -0.39 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.006 0.001 HIS B 719 PHE 0.017 0.002 PHE A 620 TYR 0.016 0.001 TYR B 441 ARG 0.006 0.000 ARG B 347 *********************** 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 177 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 0.937 Fit side-chains REVERT: A 363 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: A 370 LYS cc_start: 0.7563 (mmtp) cc_final: 0.7331 (mmtm) REVERT: A 479 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 596 LYS cc_start: 0.8469 (mttt) cc_final: 0.8124 (mtpt) REVERT: A 809 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8176 (mt) REVERT: B 370 LYS cc_start: 0.7556 (mmtp) cc_final: 0.7323 (mmtm) REVERT: B 479 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 596 LYS cc_start: 0.8443 (mttt) cc_final: 0.8085 (mtpt) REVERT: B 809 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 34 outliers final: 22 residues processed: 165 average time/residue: 1.1176 time to fit residues: 200.0305 Evaluate side-chains 168 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11004 Z= 0.211 Angle : 0.500 7.085 14934 Z= 0.253 Chirality : 0.039 0.155 1764 Planarity : 0.004 0.048 1828 Dihedral : 3.972 19.256 1462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.91 % Allowed : 17.64 % 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: 1.84 (0.23), residues: 1324 helix: 2.04 (0.18), residues: 832 sheet: 0.50 (0.44), residues: 112 loop : -0.37 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 515 HIS 0.005 0.001 HIS B 192 PHE 0.016 0.001 PHE B 620 TYR 0.015 0.001 TYR B 441 ARG 0.006 0.000 ARG A 347 *********************** 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 178 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.216 Fit side-chains REVERT: A 363 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 596 LYS cc_start: 0.8471 (mttt) cc_final: 0.8142 (mtpt) REVERT: A 809 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 479 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 596 LYS cc_start: 0.8437 (mttt) cc_final: 0.8089 (mtpt) REVERT: B 809 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 34 outliers final: 23 residues processed: 164 average time/residue: 1.0028 time to fit residues: 179.2344 Evaluate side-chains 166 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11004 Z= 0.173 Angle : 0.485 7.009 14934 Z= 0.244 Chirality : 0.039 0.151 1764 Planarity : 0.004 0.047 1828 Dihedral : 3.849 17.960 1462 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 18.84 % Favored : 79.02 % 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: 1.96 (0.23), residues: 1324 helix: 2.11 (0.18), residues: 832 sheet: 0.63 (0.45), residues: 112 loop : -0.29 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 515 HIS 0.004 0.001 HIS B 192 PHE 0.015 0.001 PHE B 620 TYR 0.013 0.001 TYR B 441 ARG 0.007 0.000 ARG A 347 ********************** 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 173 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.236 Fit side-chains REVERT: A 363 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: A 596 LYS cc_start: 0.8464 (mttt) cc_final: 0.8158 (mtpt) REVERT: B 482 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8878 (p) REVERT: B 596 LYS cc_start: 0.8423 (mttt) cc_final: 0.8099 (mtpt) REVERT: B 809 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8151 (mt) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 1.0731 time to fit residues: 188.3087 Evaluate side-chains 163 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.093539 restraints weight = 12864.350| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.71 r_work: 0.2837 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 11004 Z= 0.516 Angle : 0.650 7.638 14934 Z= 0.328 Chirality : 0.046 0.173 1764 Planarity : 0.005 0.048 1828 Dihedral : 4.368 22.046 1462 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.57 % Allowed : 18.32 % Favored : 79.11 % 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: 1.34 (0.23), residues: 1324 helix: 1.63 (0.17), residues: 834 sheet: 0.31 (0.43), residues: 112 loop : -0.54 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 515 HIS 0.010 0.002 HIS B 719 PHE 0.021 0.002 PHE A 858 TYR 0.021 0.002 TYR B 441 ARG 0.012 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4058.30 seconds wall clock time: 77 minutes 45.95 seconds (4665.95 seconds total)