Starting phenix.real_space_refine on Mon Apr 8 06:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/04_2024/8twv_41672_updated.pdb" } resolution = 3.4 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= 0.009 sd= 0.220 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 25 5.16 5 C 8305 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.88, per 1000 atoms: 0.54 Number of scatterers: 12720 At special positions: 0 Unit cell: (92.352, 91.168, 124.32, 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 25 16.00 O 2275 8.00 N 2115 7.00 C 8305 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: 4.87 Conformation dependent library (CDL) restraints added in 2.2 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 20 sheets defined 31.6% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.961A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 4.344A pdb=" N THR A 249 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 250 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 286 Processing helix chain 'A' and resid 299 through 319 removed outlier: 4.773A pdb=" N PHE A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.532A pdb=" N VAL A 314 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 222 Processing helix chain 'E' and resid 228 through 244 removed outlier: 3.961A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 252 removed outlier: 4.345A pdb=" N THR E 249 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 250 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 286 Processing helix chain 'E' and resid 299 through 319 removed outlier: 4.774A pdb=" N PHE E 304 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.531A pdb=" N VAL E 314 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.961A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.345A pdb=" N THR B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 250 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 286 Processing helix chain 'B' and resid 299 through 319 removed outlier: 4.773A pdb=" N PHE B 304 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.532A pdb=" N VAL B 314 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 228 through 244 removed outlier: 3.960A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 4.344A pdb=" N THR D 249 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 250 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 286 Processing helix chain 'D' and resid 299 through 319 removed outlier: 4.774A pdb=" N PHE D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.532A pdb=" N VAL D 314 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 228 through 244 removed outlier: 3.961A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.344A pdb=" N THR C 249 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 250 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 286 Processing helix chain 'C' and resid 299 through 319 removed outlier: 4.773A pdb=" N PHE C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.532A pdb=" N VAL C 314 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 148 removed outlier: 7.017A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'A' and resid 166 through 174 Processing sheet with id= E, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'E' and resid 145 through 148 removed outlier: 7.017A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'E' and resid 166 through 174 Processing sheet with id= I, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'B' and resid 145 through 148 removed outlier: 7.017A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'B' and resid 166 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.017A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'D' and resid 166 through 174 Processing sheet with id= Q, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'C' and resid 145 through 148 removed outlier: 7.017A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'C' and resid 166 through 174 560 hydrogen bonds defined for protein. 1425 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: 3.86 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4020 1.34 - 1.46: 2849 1.46 - 1.57: 6146 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 13065 Sorted by residual: bond pdb=" CA PHE B 208 " pdb=" CB PHE B 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.10e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.07e+00 bond pdb=" CA PHE E 208 " pdb=" CB PHE E 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.06e+00 bond pdb=" CA PHE C 208 " pdb=" CB PHE C 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.02e+00 bond pdb=" CA PHE D 208 " pdb=" CB PHE D 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.01e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.94: 280 105.94 - 112.99: 6777 112.99 - 120.04: 4668 120.04 - 127.09: 5881 127.09 - 134.15: 174 Bond angle restraints: 17780 Sorted by residual: angle pdb=" N ARG D 299 " pdb=" CA ARG D 299 " pdb=" C ARG D 299 " ideal model delta sigma weight residual 113.20 107.78 5.42 1.21e+00 6.83e-01 2.01e+01 angle pdb=" N ARG B 299 " pdb=" CA ARG B 299 " pdb=" C ARG B 299 " ideal model delta sigma weight residual 113.20 107.81 5.39 1.21e+00 6.83e-01 1.99e+01 angle pdb=" N ARG A 299 " pdb=" CA ARG A 299 " pdb=" C ARG A 299 " ideal model delta sigma weight residual 113.20 107.82 5.38 1.21e+00 6.83e-01 1.98e+01 angle pdb=" N ARG C 299 " pdb=" CA ARG C 299 " pdb=" C ARG C 299 " ideal model delta sigma weight residual 113.20 107.83 5.37 1.21e+00 6.83e-01 1.97e+01 angle pdb=" N ARG E 299 " pdb=" CA ARG E 299 " pdb=" C ARG E 299 " ideal model delta sigma weight residual 113.20 107.86 5.34 1.21e+00 6.83e-01 1.95e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6675 17.64 - 35.27: 696 35.27 - 52.91: 179 52.91 - 70.55: 45 70.55 - 88.19: 10 Dihedral angle restraints: 7605 sinusoidal: 3060 harmonic: 4545 Sorted by residual: dihedral pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " pdb=" OD1 ASP D 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.59 58.59 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " pdb=" OD1 ASP B 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.58 58.58 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " pdb=" OD1 ASP E 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1255 0.042 - 0.083: 446 0.083 - 0.125: 201 0.125 - 0.166: 38 0.166 - 0.208: 15 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA THR A 61 " pdb=" N THR A 61 " pdb=" C THR A 61 " pdb=" CB THR A 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR D 61 " pdb=" N THR D 61 " pdb=" C THR D 61 " pdb=" CB THR D 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1952 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.63e+00 pdb=" CG PHE C 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE B 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE E 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 208 " -0.000 2.00e-02 2.50e+03 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2503 2.78 - 3.31: 11394 3.31 - 3.84: 21233 3.84 - 4.37: 25150 4.37 - 4.90: 43584 Nonbonded interactions: 103864 Sorted by model distance: nonbonded pdb=" OE2 GLU D 59 " pdb=" OG SER C 134 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER D 134 " model vdw 2.256 2.440 nonbonded pdb=" O THR E 61 " pdb=" OG1 THR E 61 " model vdw 2.303 2.440 nonbonded pdb=" O THR A 61 " pdb=" OG1 THR A 61 " model vdw 2.304 2.440 nonbonded pdb=" O THR B 61 " pdb=" OG1 THR B 61 " model vdw 2.304 2.440 ... (remaining 103859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 2.070 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.580 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.004 0.054 13065 Z= 0.263 Angle : 0.727 8.046 17780 Z= 0.437 Chirality : 0.053 0.208 1955 Planarity : 0.005 0.062 2265 Dihedral : 15.797 88.185 4675 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 19.13 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1540 helix: -1.61 (0.19), residues: 525 sheet: 1.36 (0.27), residues: 430 loop : -2.25 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.006 0.001 HIS A 285 PHE 0.040 0.002 PHE B 208 TYR 0.009 0.001 TYR B 38 ARG 0.010 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6411 (mpt-90) REVERT: E 34 LYS cc_start: 0.8971 (mttp) cc_final: 0.8762 (mttm) REVERT: E 208 PHE cc_start: 0.8704 (t80) cc_final: 0.8396 (t80) REVERT: E 230 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6983 (mp0) REVERT: E 231 ARG cc_start: 0.6850 (mtm180) cc_final: 0.6450 (mpt-90) REVERT: B 225 LEU cc_start: 0.8615 (mp) cc_final: 0.8385 (mp) REVERT: B 231 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6335 (mpt-90) REVERT: D 86 ASP cc_start: 0.8750 (t70) cc_final: 0.8482 (t70) REVERT: D 230 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7121 (mp0) REVERT: D 231 ARG cc_start: 0.6980 (mtm180) cc_final: 0.6661 (mpt-90) REVERT: C 113 ASP cc_start: 0.8233 (m-30) cc_final: 0.7625 (p0) REVERT: C 208 PHE cc_start: 0.8676 (t80) cc_final: 0.8473 (t80) REVERT: C 231 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6369 (mpt-90) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2591 time to fit residues: 54.1469 Evaluate side-chains 116 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13065 Z= 0.259 Angle : 0.534 8.221 17780 Z= 0.270 Chirality : 0.046 0.144 1955 Planarity : 0.003 0.023 2265 Dihedral : 4.424 15.788 1715 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.96 % Allowed : 20.51 % Favored : 76.53 % 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: -0.92 (0.22), residues: 1540 helix: -0.72 (0.22), residues: 555 sheet: 1.33 (0.26), residues: 435 loop : -2.09 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.010 0.001 PHE A 208 TYR 0.011 0.001 TYR D 38 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 LYS cc_start: 0.9054 (mttp) cc_final: 0.8841 (mttm) REVERT: E 208 PHE cc_start: 0.8970 (t80) cc_final: 0.8625 (t80) REVERT: E 264 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: B 34 LYS cc_start: 0.9089 (mttp) cc_final: 0.8883 (mttm) REVERT: B 86 ASP cc_start: 0.8742 (t70) cc_final: 0.8306 (t70) REVERT: B 151 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7905 (m110) REVERT: B 225 LEU cc_start: 0.8821 (mp) cc_final: 0.8530 (mp) REVERT: B 231 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6030 (mpt-90) REVERT: D 231 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6785 (mtt-85) REVERT: D 264 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: C 136 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8389 (p0) REVERT: C 151 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8217 (t0) REVERT: C 161 TRP cc_start: 0.8214 (m-10) cc_final: 0.7426 (m100) REVERT: C 225 LEU cc_start: 0.8818 (mp) cc_final: 0.8613 (mp) outliers start: 41 outliers final: 18 residues processed: 172 average time/residue: 0.2563 time to fit residues: 63.8012 Evaluate side-chains 149 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 0.0040 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.4910 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13065 Z= 0.122 Angle : 0.453 6.553 17780 Z= 0.228 Chirality : 0.044 0.141 1955 Planarity : 0.003 0.020 2265 Dihedral : 4.001 15.399 1715 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 21.66 % Favored : 76.75 % 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: -0.56 (0.22), residues: 1540 helix: -0.15 (0.24), residues: 525 sheet: 1.42 (0.27), residues: 430 loop : -2.00 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.007 0.001 PHE A 208 TYR 0.010 0.001 TYR D 38 ARG 0.003 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: E 34 LYS cc_start: 0.8985 (mttp) cc_final: 0.8740 (mttm) REVERT: E 86 ASP cc_start: 0.8731 (t70) cc_final: 0.8349 (t70) REVERT: B 30 GLU cc_start: 0.8715 (pm20) cc_final: 0.8451 (pm20) REVERT: B 34 LYS cc_start: 0.9023 (mttp) cc_final: 0.8739 (mttm) REVERT: B 86 ASP cc_start: 0.8802 (t70) cc_final: 0.8451 (t70) REVERT: B 225 LEU cc_start: 0.8826 (mp) cc_final: 0.8605 (mp) REVERT: B 231 ARG cc_start: 0.7082 (mtm180) cc_final: 0.6501 (mtt-85) REVERT: D 30 GLU cc_start: 0.8783 (pm20) cc_final: 0.8491 (pm20) REVERT: D 136 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8351 (p0) REVERT: D 231 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6641 (mtm-85) REVERT: C 161 TRP cc_start: 0.8028 (m-10) cc_final: 0.7258 (m100) REVERT: C 225 LEU cc_start: 0.8894 (mp) cc_final: 0.8680 (mp) REVERT: C 247 PHE cc_start: 0.9001 (m-80) cc_final: 0.8679 (m-80) outliers start: 22 outliers final: 15 residues processed: 167 average time/residue: 0.2424 time to fit residues: 59.4060 Evaluate side-chains 145 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN E 21 ASN E 298 GLN B 298 GLN D 298 GLN C 298 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13065 Z= 0.320 Angle : 0.535 7.276 17780 Z= 0.274 Chirality : 0.046 0.137 1955 Planarity : 0.003 0.020 2265 Dihedral : 4.400 19.003 1715 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.32 % Allowed : 20.36 % Favored : 76.32 % 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: -0.44 (0.22), residues: 1540 helix: 0.07 (0.24), residues: 525 sheet: 1.28 (0.26), residues: 435 loop : -1.90 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.003 0.001 HIS A 285 PHE 0.009 0.001 PHE C 133 TYR 0.012 0.002 TYR E 204 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9036 (mt) REVERT: A 264 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: E 34 LYS cc_start: 0.9048 (mttp) cc_final: 0.8842 (mttm) REVERT: B 169 HIS cc_start: 0.7611 (t70) cc_final: 0.7363 (t70) REVERT: B 225 LEU cc_start: 0.8745 (mp) cc_final: 0.8435 (mp) REVERT: D 136 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8437 (p0) REVERT: D 151 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8012 (m110) REVERT: D 223 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: C 151 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8356 (t0) REVERT: C 161 TRP cc_start: 0.8297 (m-10) cc_final: 0.7392 (m100) REVERT: C 225 LEU cc_start: 0.8977 (mp) cc_final: 0.8654 (mp) REVERT: C 239 MET cc_start: 0.8622 (ttt) cc_final: 0.8374 (ttt) outliers start: 46 outliers final: 26 residues processed: 179 average time/residue: 0.2313 time to fit residues: 61.0489 Evaluate side-chains 159 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.0030 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13065 Z= 0.227 Angle : 0.493 8.691 17780 Z= 0.250 Chirality : 0.045 0.134 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.227 16.479 1715 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.83 % Allowed : 20.07 % Favored : 76.10 % 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: -0.33 (0.22), residues: 1540 helix: 0.17 (0.24), residues: 525 sheet: 1.17 (0.26), residues: 455 loop : -1.79 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 206 HIS 0.003 0.001 HIS A 285 PHE 0.018 0.001 PHE D 208 TYR 0.010 0.001 TYR E 245 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7720 (tpp80) REVERT: A 191 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8972 (mt) REVERT: A 245 TYR cc_start: 0.8145 (m-10) cc_final: 0.7516 (m-10) REVERT: A 264 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: E 34 LYS cc_start: 0.9058 (mttp) cc_final: 0.8835 (mttm) REVERT: E 65 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7514 (tmm-80) REVERT: E 231 ARG cc_start: 0.7460 (mtm180) cc_final: 0.6836 (mtm180) REVERT: B 34 LYS cc_start: 0.9093 (mttp) cc_final: 0.8887 (mttm) REVERT: B 151 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7879 (m110) REVERT: B 169 HIS cc_start: 0.7649 (t70) cc_final: 0.7400 (t70) REVERT: B 225 LEU cc_start: 0.8829 (mp) cc_final: 0.8602 (mp) REVERT: B 231 ARG cc_start: 0.7313 (mtm180) cc_final: 0.6856 (mtt180) REVERT: D 30 GLU cc_start: 0.8958 (pm20) cc_final: 0.8614 (pm20) REVERT: D 65 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7371 (ttt180) REVERT: D 136 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8391 (p0) REVERT: D 223 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: D 264 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: C 30 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: C 136 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8385 (p0) REVERT: C 161 TRP cc_start: 0.8257 (m-10) cc_final: 0.7354 (m100) REVERT: C 184 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8124 (m-40) REVERT: C 225 LEU cc_start: 0.8773 (mp) cc_final: 0.8362 (mp) REVERT: C 239 MET cc_start: 0.8601 (ttt) cc_final: 0.8330 (ttt) outliers start: 53 outliers final: 33 residues processed: 175 average time/residue: 0.2566 time to fit residues: 64.9047 Evaluate side-chains 170 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 236 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13065 Z= 0.315 Angle : 0.536 8.697 17780 Z= 0.274 Chirality : 0.046 0.132 1955 Planarity : 0.003 0.018 2265 Dihedral : 4.450 20.323 1715 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.33 % Allowed : 19.93 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1540 helix: 0.18 (0.24), residues: 525 sheet: 1.07 (0.26), residues: 455 loop : -1.75 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.003 0.001 HIS A 285 PHE 0.018 0.001 PHE B 208 TYR 0.013 0.002 TYR E 245 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 135 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7720 (tpp80) REVERT: A 161 TRP cc_start: 0.8388 (m-10) cc_final: 0.7459 (m-90) REVERT: A 191 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9023 (mt) REVERT: A 208 PHE cc_start: 0.9121 (t80) cc_final: 0.8907 (t80) REVERT: A 220 TRP cc_start: 0.7731 (m-10) cc_final: 0.7479 (m-10) REVERT: A 245 TYR cc_start: 0.8399 (m-10) cc_final: 0.7906 (m-10) REVERT: A 248 TYR cc_start: 0.8931 (t80) cc_final: 0.8583 (t80) REVERT: A 264 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: E 34 LYS cc_start: 0.9091 (mttp) cc_final: 0.8882 (mttm) REVERT: E 65 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7790 (ttm-80) REVERT: E 231 ARG cc_start: 0.7426 (mtm180) cc_final: 0.7161 (mtm180) REVERT: E 264 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: B 30 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: B 151 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7969 (m110) REVERT: B 169 HIS cc_start: 0.7581 (t70) cc_final: 0.7339 (t70) REVERT: D 30 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: D 65 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7460 (ttt180) REVERT: D 136 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8430 (p0) REVERT: D 151 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8030 (m110) REVERT: D 223 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: D 264 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: C 30 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: C 136 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8430 (p0) REVERT: C 161 TRP cc_start: 0.8357 (m-10) cc_final: 0.8074 (m-90) REVERT: C 184 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8044 (m-40) REVERT: C 239 MET cc_start: 0.8628 (ttt) cc_final: 0.8377 (ttt) outliers start: 60 outliers final: 36 residues processed: 186 average time/residue: 0.2442 time to fit residues: 66.6065 Evaluate side-chains 184 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 134 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13065 Z= 0.207 Angle : 0.486 8.165 17780 Z= 0.246 Chirality : 0.045 0.131 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.185 15.559 1715 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.12 % Allowed : 20.14 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1540 helix: 0.53 (0.25), residues: 495 sheet: 1.15 (0.26), residues: 450 loop : -1.85 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 206 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.001 PHE D 208 TYR 0.009 0.001 TYR B 245 ARG 0.002 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 136 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: A 65 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7617 (tpp80) REVERT: A 113 ASP cc_start: 0.8304 (m-30) cc_final: 0.7831 (p0) REVERT: A 129 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: A 151 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8038 (m110) REVERT: A 161 TRP cc_start: 0.8252 (m-10) cc_final: 0.7381 (m-90) REVERT: A 191 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8977 (mt) REVERT: A 220 TRP cc_start: 0.7686 (m-10) cc_final: 0.7421 (m-10) REVERT: A 245 TYR cc_start: 0.8335 (m-10) cc_final: 0.7832 (m-10) REVERT: E 30 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: E 34 LYS cc_start: 0.9085 (mttp) cc_final: 0.8861 (mttm) REVERT: E 65 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7807 (ttm-80) REVERT: E 231 ARG cc_start: 0.7346 (mtm180) cc_final: 0.7039 (mtm180) REVERT: E 264 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: B 30 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: B 129 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 169 HIS cc_start: 0.7635 (t70) cc_final: 0.7389 (t70) REVERT: D 30 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: D 65 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7384 (ttt180) REVERT: D 136 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8384 (p0) REVERT: D 223 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: D 231 ARG cc_start: 0.7159 (mtm180) cc_final: 0.6943 (mtm-85) REVERT: D 264 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: C 30 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8435 (pm20) REVERT: C 136 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8405 (p0) REVERT: C 161 TRP cc_start: 0.8312 (m-10) cc_final: 0.7406 (m100) REVERT: C 184 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8096 (m-40) REVERT: C 239 MET cc_start: 0.8594 (ttt) cc_final: 0.8287 (ttt) outliers start: 57 outliers final: 34 residues processed: 183 average time/residue: 0.2442 time to fit residues: 65.3136 Evaluate side-chains 182 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13065 Z= 0.273 Angle : 0.517 7.940 17780 Z= 0.262 Chirality : 0.045 0.131 1955 Planarity : 0.003 0.018 2265 Dihedral : 4.307 18.572 1715 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.26 % Allowed : 20.29 % Favored : 75.45 % 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: -0.33 (0.23), residues: 1540 helix: 0.23 (0.24), residues: 525 sheet: 1.09 (0.25), residues: 455 loop : -1.77 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 161 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.001 PHE A 208 TYR 0.019 0.001 TYR E 248 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 129 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (pm20) REVERT: A 65 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7692 (tpp80) REVERT: A 129 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: A 151 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8070 (m110) REVERT: A 161 TRP cc_start: 0.8259 (m-10) cc_final: 0.7371 (m-90) REVERT: A 191 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9007 (mt) REVERT: A 220 TRP cc_start: 0.7704 (m-10) cc_final: 0.7447 (m-10) REVERT: A 245 TYR cc_start: 0.8406 (m-10) cc_final: 0.7927 (m-10) REVERT: E 30 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: E 34 LYS cc_start: 0.9092 (mttp) cc_final: 0.8875 (mttm) REVERT: E 65 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: E 264 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: B 30 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: B 129 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: B 151 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7960 (m110) REVERT: B 169 HIS cc_start: 0.7605 (t70) cc_final: 0.7382 (t70) REVERT: D 30 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: D 65 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7386 (ttt180) REVERT: D 136 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8442 (p0) REVERT: D 223 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: D 231 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6950 (mtm-85) REVERT: D 264 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: C 30 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: C 136 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8426 (p0) REVERT: C 151 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8201 (m110) REVERT: C 161 TRP cc_start: 0.8372 (m-10) cc_final: 0.8108 (m-90) REVERT: C 184 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: C 239 MET cc_start: 0.8621 (ttt) cc_final: 0.8353 (ttt) outliers start: 59 outliers final: 36 residues processed: 178 average time/residue: 0.2478 time to fit residues: 64.1915 Evaluate side-chains 184 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.0270 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 154 ASN C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13065 Z= 0.158 Angle : 0.473 7.418 17780 Z= 0.238 Chirality : 0.044 0.131 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.041 14.245 1715 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.26 % Allowed : 20.43 % Favored : 75.31 % 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: -0.20 (0.22), residues: 1540 helix: 0.58 (0.25), residues: 495 sheet: 1.20 (0.26), residues: 450 loop : -1.87 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 161 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.001 PHE A 208 TYR 0.016 0.001 TYR E 248 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 139 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: A 113 ASP cc_start: 0.8241 (m-30) cc_final: 0.7785 (p0) REVERT: A 129 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: A 151 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8018 (m110) REVERT: A 161 TRP cc_start: 0.8252 (m-10) cc_final: 0.7498 (m-90) REVERT: A 191 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8952 (mt) REVERT: A 245 TYR cc_start: 0.8349 (m-10) cc_final: 0.7942 (m-10) REVERT: E 30 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: E 34 LYS cc_start: 0.9016 (mttp) cc_final: 0.8756 (mttm) REVERT: E 65 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7787 (ttm-80) REVERT: E 231 ARG cc_start: 0.7402 (ttm170) cc_final: 0.6831 (mtt180) REVERT: B 30 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: B 129 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: B 151 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7903 (m110) REVERT: D 30 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: D 65 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7352 (ttt180) REVERT: D 136 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8386 (p0) REVERT: D 151 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8122 (m110) REVERT: D 223 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: D 264 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: C 30 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: C 136 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8408 (p0) REVERT: C 151 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8155 (m110) REVERT: C 161 TRP cc_start: 0.8265 (m-10) cc_final: 0.7483 (m-90) REVERT: C 184 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: C 239 MET cc_start: 0.8579 (ttt) cc_final: 0.8268 (ttt) outliers start: 59 outliers final: 35 residues processed: 182 average time/residue: 0.2438 time to fit residues: 64.9430 Evaluate side-chains 187 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 134 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13065 Z= 0.457 Angle : 0.602 8.214 17780 Z= 0.309 Chirality : 0.048 0.142 1955 Planarity : 0.003 0.018 2265 Dihedral : 4.629 23.966 1715 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.77 % Allowed : 20.00 % Favored : 75.23 % 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: -0.32 (0.23), residues: 1540 helix: 0.48 (0.25), residues: 490 sheet: 1.00 (0.26), residues: 455 loop : -1.80 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 161 HIS 0.003 0.001 HIS A 177 PHE 0.024 0.001 PHE A 208 TYR 0.025 0.002 TYR B 248 ARG 0.002 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 135 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: A 129 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: A 161 TRP cc_start: 0.8321 (m-10) cc_final: 0.7478 (m-90) REVERT: A 191 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9071 (mt) REVERT: A 220 TRP cc_start: 0.7768 (m-10) cc_final: 0.7523 (m-10) REVERT: A 245 TYR cc_start: 0.8528 (m-10) cc_final: 0.8083 (m-10) REVERT: A 248 TYR cc_start: 0.8932 (t80) cc_final: 0.8674 (t80) REVERT: E 30 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: E 65 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: E 264 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8425 (mt0) REVERT: B 30 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: B 129 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 151 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8080 (m110) REVERT: B 231 ARG cc_start: 0.7270 (mtm180) cc_final: 0.6799 (mtt180) REVERT: D 30 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: D 65 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7455 (ttt180) REVERT: D 136 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8452 (p0) REVERT: D 151 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: D 223 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: C 30 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: C 136 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8504 (p0) REVERT: C 151 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8231 (m-40) REVERT: C 161 TRP cc_start: 0.8438 (m-10) cc_final: 0.8173 (m-90) REVERT: C 184 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: C 239 MET cc_start: 0.8658 (ttt) cc_final: 0.8422 (ttt) outliers start: 66 outliers final: 37 residues processed: 186 average time/residue: 0.2424 time to fit residues: 65.9476 Evaluate side-chains 186 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 154 ASN D 154 ASN D 264 GLN C 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.095180 restraints weight = 16022.638| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.68 r_work: 0.2823 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13065 Z= 0.233 Angle : 0.513 7.836 17780 Z= 0.260 Chirality : 0.045 0.134 1955 Planarity : 0.003 0.018 2265 Dihedral : 4.315 17.073 1715 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.33 % Allowed : 20.58 % Favored : 75.09 % 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: -0.30 (0.23), residues: 1540 helix: 0.53 (0.25), residues: 495 sheet: 1.17 (0.26), residues: 430 loop : -1.88 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 161 HIS 0.003 0.001 HIS A 285 PHE 0.020 0.001 PHE A 208 TYR 0.021 0.001 TYR B 248 ARG 0.002 0.000 ARG D 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.62 seconds wall clock time: 47 minutes 23.70 seconds (2843.70 seconds total)