Starting phenix.real_space_refine on Tue Nov 14 10:22:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwh_21416/11_2023/6vwh_21416.pdb" } resolution = 4.26 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= 0.022 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 2726 2.51 5 N 750 2.21 5 O 808 1.98 5 H 4139 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 772": "OD1" <-> "OD2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 799": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 8461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2196 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain breaks: 2 Chain: "B" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6265 Classifications: {'peptide': 403} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 377} Chain breaks: 4 Time building chain proxies: 4.15, per 1000 atoms: 0.49 Number of scatterers: 8461 At special positions: 0 Unit cell: (97.52, 119.78, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 808 8.00 N 750 7.00 C 2726 6.00 H 4139 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.02 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.04 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: 7.38 Conformation dependent library (CDL) restraints added in 841.8 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 11.3% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.717A pdb=" N TYR A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.529A pdb=" N LEU B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 17' Processing helix chain 'B' and resid 18 through 22 removed outlier: 4.334A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.965A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.919A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.536A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 769 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 793 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.609A pdb=" N ILE B 25 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.735A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 209 removed outlier: 8.147A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 248 removed outlier: 3.664A pdb=" N ARG B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 590 removed outlier: 4.801A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 747 through 751 removed outlier: 4.145A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS B 776 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 791 " --> pdb=" O ILE B 771 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 249 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: 2.93 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4137 1.04 - 1.24: 526 1.24 - 1.44: 1429 1.44 - 1.64: 2432 1.64 - 1.84: 44 Bond restraints: 8568 Sorted by residual: bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.57e+00 bond pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" N ASN A 577 " pdb=" H ASN A 577 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N GLU A 682 " pdb=" CA GLU A 682 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.09e+00 bond pdb=" C ARG B 620 " pdb=" N GLN B 621 " ideal model delta sigma weight residual 1.340 1.260 0.080 5.87e-02 2.90e+02 1.87e+00 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 329 107.06 - 113.80: 9767 113.80 - 120.55: 2895 120.55 - 127.29: 2366 127.29 - 134.04: 56 Bond angle restraints: 15413 Sorted by residual: angle pdb=" N ASN B 94 " pdb=" CA ASN B 94 " pdb=" C ASN B 94 " ideal model delta sigma weight residual 113.28 120.89 -7.61 1.57e+00 4.06e-01 2.35e+01 angle pdb=" N ASN B 94 " pdb=" CA ASN B 94 " pdb=" CB ASN B 94 " ideal model delta sigma weight residual 114.17 108.88 5.29 1.14e+00 7.69e-01 2.16e+01 angle pdb=" N LEU B 256 " pdb=" CA LEU B 256 " pdb=" C LEU B 256 " ideal model delta sigma weight residual 110.20 103.33 6.87 1.58e+00 4.01e-01 1.89e+01 angle pdb=" N ASN B 602 " pdb=" CA ASN B 602 " pdb=" C ASN B 602 " ideal model delta sigma weight residual 110.10 115.17 -5.07 1.53e+00 4.27e-01 1.10e+01 angle pdb=" CA TYR B 628 " pdb=" CB TYR B 628 " pdb=" CG TYR B 628 " ideal model delta sigma weight residual 113.90 119.31 -5.41 1.80e+00 3.09e-01 9.04e+00 ... (remaining 15408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3241 17.84 - 35.68: 210 35.68 - 53.52: 52 53.52 - 71.36: 31 71.36 - 89.20: 5 Dihedral angle restraints: 3539 sinusoidal: 1636 harmonic: 1903 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -141.70 55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CA SER A 788 " pdb=" C SER A 788 " pdb=" N ASN A 789 " pdb=" CA ASN A 789 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 788 " pdb=" C SER B 788 " pdb=" N ASN B 789 " pdb=" CA ASN B 789 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 3536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 362 0.045 - 0.089: 194 0.089 - 0.134: 68 0.134 - 0.179: 13 0.179 - 0.223: 3 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA PHE B 766 " pdb=" N PHE B 766 " pdb=" C PHE B 766 " pdb=" CB PHE B 766 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASN B 94 " pdb=" N ASN B 94 " pdb=" C ASN B 94 " pdb=" CB ASN B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CB ILE B 615 " pdb=" CA ILE B 615 " pdb=" CG1 ILE B 615 " pdb=" CG2 ILE B 615 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 637 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 770 " -0.095 9.50e-02 1.11e+02 4.64e-02 2.69e+01 pdb=" NE ARG A 770 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 770 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG A 770 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG A 770 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG A 770 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 770 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 770 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 770 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 283 " 0.060 9.50e-02 1.11e+02 3.92e-02 2.60e+01 pdb=" NE ARG B 283 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 283 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 283 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG B 283 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG B 283 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG B 283 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARG B 283 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 283 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 689 " 0.034 9.50e-02 1.11e+02 3.42e-02 2.36e+01 pdb=" NE ARG A 689 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 689 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 689 " -0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG A 689 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 689 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 689 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 689 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 689 " -0.019 2.00e-02 2.50e+03 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 273 2.10 - 2.72: 14639 2.72 - 3.35: 23897 3.35 - 3.97: 29803 3.97 - 4.60: 46113 Nonbonded interactions: 114725 Sorted by model distance: nonbonded pdb=" O TYR B 614 " pdb=" H VAL B 752 " model vdw 1.470 1.850 nonbonded pdb=" O TYR A 626 " pdb=" H TYR A 628 " model vdw 1.485 1.850 nonbonded pdb=" HG SER B 257 " pdb=" O GLU B 264 " model vdw 1.490 1.850 nonbonded pdb=" O ARG A 764 " pdb=" HG1 THR A 767 " model vdw 1.517 1.850 nonbonded pdb=" O TYR B 626 " pdb=" H TYR B 628 " model vdw 1.517 1.850 ... (remaining 114720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.020 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: 0.100 Extract box with map and model: 13.730 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 31.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.006 0.080 4429 Z= 0.362 Angle : 1.063 7.731 6010 Z= 0.612 Chirality : 0.058 0.223 640 Planarity : 0.005 0.053 787 Dihedral : 13.745 89.202 1642 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.69 % Favored : 92.54 % Rotamer: Outliers : 0.82 % Allowed : 5.97 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.73 (0.34), residues: 523 helix: -3.57 (0.58), residues: 40 sheet: -0.34 (0.46), residues: 131 loop : -1.21 (0.30), residues: 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 0.4096 time to fit residues: 44.6086 Evaluate side-chains 54 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0975 time to fit residues: 1.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 HIS B 14 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4429 Z= 0.229 Angle : 0.680 5.469 6010 Z= 0.372 Chirality : 0.048 0.161 640 Planarity : 0.004 0.036 787 Dihedral : 6.909 27.542 597 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.74 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.35), residues: 523 helix: -3.13 (0.59), residues: 43 sheet: -0.68 (0.43), residues: 130 loop : -0.70 (0.33), residues: 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2750 time to fit residues: 23.9197 Evaluate side-chains 43 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 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 621 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4429 Z= 0.261 Angle : 0.650 4.644 6010 Z= 0.356 Chirality : 0.047 0.140 640 Planarity : 0.004 0.039 787 Dihedral : 6.452 28.079 597 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.07 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.31 (0.35), residues: 523 helix: -2.54 (0.67), residues: 28 sheet: -0.95 (0.44), residues: 123 loop : -0.70 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2596 time to fit residues: 19.8028 Evaluate side-chains 46 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 45 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN B 136 ASN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4429 Z= 0.137 Angle : 0.550 3.962 6010 Z= 0.294 Chirality : 0.045 0.143 640 Planarity : 0.004 0.038 787 Dihedral : 5.770 24.409 597 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.16 % Favored : 94.26 % Rotamer: Outliers : 0.21 % Allowed : 1.44 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.03 (0.36), residues: 523 helix: -1.16 (0.82), residues: 28 sheet: -0.96 (0.44), residues: 128 loop : -0.51 (0.33), residues: 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2729 time to fit residues: 22.6395 Evaluate side-chains 49 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4429 Z= 0.229 Angle : 0.600 5.305 6010 Z= 0.324 Chirality : 0.046 0.141 640 Planarity : 0.004 0.030 787 Dihedral : 5.762 26.668 597 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.60 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.30 (0.37), residues: 523 helix: -1.39 (0.77), residues: 28 sheet: -1.30 (0.43), residues: 126 loop : -0.63 (0.34), residues: 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2919 time to fit residues: 23.7750 Evaluate side-chains 47 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 136 ASN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4429 Z= 0.194 Angle : 0.575 4.734 6010 Z= 0.309 Chirality : 0.045 0.161 640 Planarity : 0.004 0.030 787 Dihedral : 5.598 24.895 597 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.03 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.43 (0.36), residues: 523 helix: -1.12 (0.81), residues: 28 sheet: -1.45 (0.43), residues: 129 loop : -0.72 (0.34), residues: 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2782 time to fit residues: 22.6086 Evaluate side-chains 45 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4429 Z= 0.193 Angle : 0.559 4.598 6010 Z= 0.301 Chirality : 0.045 0.145 640 Planarity : 0.004 0.031 787 Dihedral : 5.472 23.904 597 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.80 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.57 (0.37), residues: 523 helix: -1.38 (0.80), residues: 28 sheet: -1.55 (0.44), residues: 128 loop : -0.81 (0.34), residues: 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2938 time to fit residues: 22.8784 Evaluate side-chains 45 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4429 Z= 0.185 Angle : 0.537 4.400 6010 Z= 0.288 Chirality : 0.045 0.147 640 Planarity : 0.004 0.030 787 Dihedral : 5.270 22.572 597 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.65 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.37 (0.37), residues: 523 helix: -1.26 (0.81), residues: 28 sheet: -1.05 (0.48), residues: 117 loop : -0.84 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2881 time to fit residues: 23.0887 Evaluate side-chains 46 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4429 Z= 0.186 Angle : 0.540 4.314 6010 Z= 0.290 Chirality : 0.044 0.141 640 Planarity : 0.004 0.031 787 Dihedral : 5.174 23.333 597 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.80 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.43 (0.37), residues: 523 helix: -1.18 (0.84), residues: 28 sheet: -1.22 (0.47), residues: 122 loop : -0.84 (0.34), residues: 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2788 time to fit residues: 21.1349 Evaluate side-chains 44 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4429 Z= 0.193 Angle : 0.548 4.532 6010 Z= 0.293 Chirality : 0.045 0.145 640 Planarity : 0.004 0.032 787 Dihedral : 5.176 22.784 597 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.99 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.37), residues: 523 helix: -1.11 (0.85), residues: 28 sheet: -1.31 (0.47), residues: 121 loop : -0.93 (0.33), residues: 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3433 time to fit residues: 25.9739 Evaluate side-chains 47 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.121783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.106659 restraints weight = 58192.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.110360 restraints weight = 29978.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.112870 restraints weight = 18443.197| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4429 Z= 0.178 Angle : 0.536 4.451 6010 Z= 0.287 Chirality : 0.044 0.141 640 Planarity : 0.004 0.032 787 Dihedral : 5.090 22.875 597 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.37 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.61 (0.37), residues: 523 helix: -0.85 (0.87), residues: 28 sheet: -1.38 (0.47), residues: 126 loop : -0.98 (0.33), residues: 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.51 seconds wall clock time: 53 minutes 36.14 seconds (3216.14 seconds total)