Starting phenix.real_space_refine on Sun Apr 7 18:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/04_2024/8twz_41673_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 7360 2.51 5 N 1850 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11270 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "C" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "D" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "E" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} 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: "B" 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} 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: "E" 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: 5.89, per 1000 atoms: 0.52 Number of scatterers: 11270 At special positions: 0 Unit cell: (89.723, 89.723, 112.424, 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 20 16.00 O 2040 8.00 N 1850 7.00 C 7360 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: 4.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 20 sheets defined 27.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.765A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.639A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 249 removed outlier: 4.110A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 283 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.766A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.640A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 249 removed outlier: 4.110A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 283 Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.765A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.639A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 249 removed outlier: 4.110A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.765A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.639A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 249 removed outlier: 4.110A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 283 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.765A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.638A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 249 removed outlier: 4.110A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 283 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: 6.946A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (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 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.946A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'B' and resid 166 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.946A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' 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: 6.946A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (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 'E' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'E' and resid 145 through 148 removed outlier: 6.946A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'E' and resid 166 through 174 480 hydrogen bonds defined for protein. 1410 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: 3.22 Time building geometry restraints manager: 4.57 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: 3286 1.34 - 1.45: 2013 1.45 - 1.57: 6246 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 11585 Sorted by residual: bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.83e+00 bond pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.58e+00 ... (remaining 11580 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.19: 395 107.19 - 113.95: 6342 113.95 - 120.70: 4697 120.70 - 127.46: 4205 127.46 - 134.21: 151 Bond angle restraints: 15790 Sorted by residual: angle pdb=" C VAL A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta sigma weight residual 122.64 116.80 5.84 1.77e+00 3.19e-01 1.09e+01 angle pdb=" C VAL B 58 " pdb=" N GLU B 59 " pdb=" CA GLU B 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 angle pdb=" C VAL D 58 " pdb=" N GLU D 59 " pdb=" CA GLU D 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 6041 15.96 - 31.92: 544 31.92 - 47.87: 115 47.87 - 63.83: 40 63.83 - 79.79: 15 Dihedral angle restraints: 6755 sinusoidal: 2715 harmonic: 4040 Sorted by residual: dihedral pdb=" CG ARG B 255 " pdb=" CD ARG B 255 " pdb=" NE ARG B 255 " pdb=" CZ ARG B 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.53 48.47 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG E 255 " pdb=" CD ARG E 255 " pdb=" NE ARG E 255 " pdb=" CZ ARG E 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.54 48.46 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG D 255 " pdb=" CD ARG D 255 " pdb=" NE ARG D 255 " pdb=" CZ ARG D 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.58 48.42 2 1.50e+01 4.44e-03 1.19e+01 ... (remaining 6752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1131 0.041 - 0.082: 399 0.082 - 0.124: 165 0.124 - 0.165: 34 0.165 - 0.206: 11 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CB THR D 149 " pdb=" CA THR D 149 " pdb=" OG1 THR D 149 " pdb=" CG2 THR D 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR C 149 " pdb=" CA THR C 149 " pdb=" OG1 THR C 149 " pdb=" CG2 THR C 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 149 " pdb=" CA THR A 149 " pdb=" OG1 THR A 149 " pdb=" CG2 THR A 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1737 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.53e+00 pdb=" NE ARG B 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 255 " -0.185 9.50e-02 1.11e+02 8.35e-02 5.52e+00 pdb=" NE ARG E 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.52e+00 pdb=" NE ARG A 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 255 " -0.000 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3379 2.83 - 3.35: 9623 3.35 - 3.86: 18831 3.86 - 4.38: 21963 4.38 - 4.90: 39599 Nonbonded interactions: 93395 Sorted by model distance: nonbonded pdb=" OH TYR A 245 " pdb=" OH TYR E 270 " model vdw 2.309 2.440 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.329 2.440 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.329 2.440 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.330 2.440 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.330 2.440 ... (remaining 93390 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: 0.280 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: 2.020 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11585 Z= 0.274 Angle : 0.715 7.466 15790 Z= 0.371 Chirality : 0.052 0.206 1740 Planarity : 0.006 0.084 2005 Dihedral : 14.021 79.790 4145 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.87 (0.22), residues: 1360 helix: -0.43 (0.23), residues: 425 sheet: 0.71 (0.25), residues: 465 loop : -2.01 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 206 HIS 0.004 0.001 HIS D 177 PHE 0.009 0.002 PHE E 116 TYR 0.013 0.001 TYR B 248 ARG 0.020 0.002 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.340 Fit side-chains REVERT: B 129 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 114 MET cc_start: 0.8537 (ttm) cc_final: 0.8286 (ttm) REVERT: C 263 ASP cc_start: 0.7575 (m-30) cc_final: 0.7285 (m-30) REVERT: D 172 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2539 time to fit residues: 67.1737 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN B 60 ASN B 89 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 89 ASN D 60 ASN D 89 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 89 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11585 Z= 0.322 Angle : 0.564 6.367 15790 Z= 0.286 Chirality : 0.048 0.137 1740 Planarity : 0.003 0.027 2005 Dihedral : 4.425 16.348 1510 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.89 % Allowed : 9.60 % Favored : 89.52 % 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: -0.58 (0.22), residues: 1360 helix: 0.37 (0.24), residues: 425 sheet: 0.74 (0.26), residues: 405 loop : -1.95 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 206 HIS 0.003 0.001 HIS B 177 PHE 0.015 0.002 PHE B 236 TYR 0.014 0.002 TYR C 248 ARG 0.005 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.354 Fit side-chains REVERT: B 236 PHE cc_start: 0.7396 (m-80) cc_final: 0.7114 (m-80) REVERT: C 97 ASP cc_start: 0.7884 (p0) cc_final: 0.7297 (p0) REVERT: D 60 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8254 (p0) REVERT: D 172 ASP cc_start: 0.8077 (m-30) cc_final: 0.7747 (m-30) REVERT: D 236 PHE cc_start: 0.7190 (m-80) cc_final: 0.6909 (m-80) REVERT: D 255 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7897 (mtt90) REVERT: E 167 SER cc_start: 0.8478 (m) cc_final: 0.8274 (p) outliers start: 11 outliers final: 8 residues processed: 185 average time/residue: 0.2547 time to fit residues: 65.3839 Evaluate side-chains 156 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11585 Z= 0.193 Angle : 0.513 8.124 15790 Z= 0.259 Chirality : 0.046 0.135 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.172 15.240 1510 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.69 % Allowed : 11.61 % Favored : 86.69 % 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: -0.49 (0.22), residues: 1360 helix: 0.59 (0.25), residues: 425 sheet: 0.69 (0.26), residues: 405 loop : -1.93 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.018 0.001 PHE E 236 TYR 0.018 0.001 TYR D 245 ARG 0.002 0.000 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.365 Fit side-chains REVERT: B 245 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7353 (t80) REVERT: C 245 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7255 (t80) REVERT: D 172 ASP cc_start: 0.8061 (m-30) cc_final: 0.7730 (m-30) outliers start: 21 outliers final: 11 residues processed: 181 average time/residue: 0.2500 time to fit residues: 64.0280 Evaluate side-chains 156 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 215 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 60 ASN D 60 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11585 Z= 0.216 Angle : 0.512 8.066 15790 Z= 0.258 Chirality : 0.047 0.133 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.087 15.285 1510 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.85 % Allowed : 14.27 % Favored : 83.87 % 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: -0.49 (0.23), residues: 1360 helix: 0.63 (0.25), residues: 425 sheet: 0.65 (0.26), residues: 405 loop : -1.94 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 206 HIS 0.003 0.001 HIS B 177 PHE 0.023 0.001 PHE E 236 TYR 0.016 0.001 TYR A 245 ARG 0.004 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.223 Fit side-chains REVERT: A 60 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (p0) REVERT: B 114 MET cc_start: 0.8399 (ttm) cc_final: 0.8088 (ttm) REVERT: B 245 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 59 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7645 (mm-30) REVERT: C 233 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6327 (tt0) REVERT: C 245 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7195 (t80) REVERT: D 60 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8504 (p0) REVERT: D 172 ASP cc_start: 0.8035 (m-30) cc_final: 0.7708 (m-30) REVERT: D 233 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6499 (tt0) outliers start: 23 outliers final: 11 residues processed: 170 average time/residue: 0.2292 time to fit residues: 55.8294 Evaluate side-chains 158 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11585 Z= 0.305 Angle : 0.536 6.648 15790 Z= 0.271 Chirality : 0.048 0.133 1740 Planarity : 0.003 0.022 2005 Dihedral : 4.245 15.870 1510 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.66 % Allowed : 15.00 % Favored : 82.34 % 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: -0.54 (0.23), residues: 1360 helix: 0.60 (0.25), residues: 425 sheet: 0.60 (0.26), residues: 405 loop : -1.95 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS B 177 PHE 0.023 0.001 PHE E 236 TYR 0.018 0.001 TYR D 245 ARG 0.004 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.348 Fit side-chains REVERT: A 60 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8562 (p0) REVERT: A 245 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 245 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6852 (t80) REVERT: C 59 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7635 (mm-30) REVERT: C 233 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6229 (tt0) REVERT: C 245 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6939 (t80) REVERT: D 60 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (p0) REVERT: D 172 ASP cc_start: 0.8042 (m-30) cc_final: 0.7750 (m-30) REVERT: D 233 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6380 (tt0) REVERT: D 255 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8050 (mtt90) REVERT: E 245 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6850 (t80) outliers start: 33 outliers final: 20 residues processed: 184 average time/residue: 0.2634 time to fit residues: 67.0981 Evaluate side-chains 174 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 68 optimal weight: 0.0270 chunk 125 optimal weight: 5.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 136 ASN A 139 GLN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 169 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11585 Z= 0.133 Angle : 0.474 6.353 15790 Z= 0.238 Chirality : 0.045 0.136 1740 Planarity : 0.003 0.028 2005 Dihedral : 3.917 15.104 1510 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.50 % Allowed : 16.05 % Favored : 81.45 % 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: -0.32 (0.23), residues: 1360 helix: 0.75 (0.25), residues: 425 sheet: 1.17 (0.27), residues: 380 loop : -2.07 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.019 0.001 PHE E 236 TYR 0.015 0.001 TYR D 245 ARG 0.006 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 1.316 Fit side-chains REVERT: A 245 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6983 (t80) REVERT: B 245 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7046 (t80) REVERT: C 233 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: C 245 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6982 (t80) REVERT: D 60 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8639 (p0) REVERT: D 172 ASP cc_start: 0.8017 (m-30) cc_final: 0.7706 (m-30) REVERT: D 233 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6224 (tt0) REVERT: E 236 PHE cc_start: 0.7157 (m-80) cc_final: 0.6932 (m-80) REVERT: E 245 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.2467 time to fit residues: 59.0391 Evaluate side-chains 167 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.0270 chunk 109 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11585 Z= 0.162 Angle : 0.482 6.270 15790 Z= 0.239 Chirality : 0.045 0.132 1740 Planarity : 0.003 0.033 2005 Dihedral : 3.841 15.141 1510 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.34 % Allowed : 16.85 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1360 helix: 0.79 (0.26), residues: 425 sheet: 0.65 (0.27), residues: 405 loop : -1.90 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.016 0.001 PHE E 236 TYR 0.015 0.001 TYR C 245 ARG 0.006 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.310 Fit side-chains REVERT: A 245 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6941 (t80) REVERT: B 239 MET cc_start: 0.7194 (tpp) cc_final: 0.6874 (ttp) REVERT: B 245 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 245 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6926 (t80) REVERT: D 172 ASP cc_start: 0.8018 (m-30) cc_final: 0.7706 (m-30) REVERT: D 255 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.8023 (mtt90) REVERT: E 236 PHE cc_start: 0.7140 (m-80) cc_final: 0.6854 (m-80) REVERT: E 245 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.6733 (t80) outliers start: 29 outliers final: 22 residues processed: 179 average time/residue: 0.2444 time to fit residues: 61.9990 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11585 Z= 0.185 Angle : 0.486 6.241 15790 Z= 0.243 Chirality : 0.046 0.131 1740 Planarity : 0.002 0.019 2005 Dihedral : 3.862 15.747 1510 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.34 % Allowed : 16.69 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1360 helix: 0.77 (0.26), residues: 425 sheet: 0.66 (0.27), residues: 405 loop : -1.91 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.003 0.001 HIS B 177 PHE 0.014 0.001 PHE E 236 TYR 0.014 0.001 TYR C 245 ARG 0.003 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.360 Fit side-chains REVERT: A 245 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 239 MET cc_start: 0.7194 (tpp) cc_final: 0.6871 (ttp) REVERT: B 245 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.6952 (t80) REVERT: C 245 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6938 (t80) REVERT: D 172 ASP cc_start: 0.8020 (m-30) cc_final: 0.7680 (m-30) REVERT: D 255 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.8028 (mtt90) REVERT: E 233 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: E 245 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6577 (t80) outliers start: 29 outliers final: 24 residues processed: 174 average time/residue: 0.2351 time to fit residues: 58.6225 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 0.0030 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 21 ASN D 27 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11585 Z= 0.152 Angle : 0.479 6.257 15790 Z= 0.238 Chirality : 0.045 0.132 1740 Planarity : 0.002 0.019 2005 Dihedral : 3.796 15.454 1510 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.73 % 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: -0.27 (0.23), residues: 1360 helix: 0.81 (0.26), residues: 425 sheet: 1.21 (0.27), residues: 380 loop : -2.06 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.008 0.001 PHE C 106 TYR 0.014 0.001 TYR C 245 ARG 0.003 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.174 Fit side-chains REVERT: A 245 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6920 (t80) REVERT: B 159 GLU cc_start: 0.7525 (pm20) cc_final: 0.7222 (pm20) REVERT: B 239 MET cc_start: 0.7155 (tpp) cc_final: 0.6856 (ttp) REVERT: B 245 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6984 (t80) REVERT: C 59 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 245 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.6929 (t80) REVERT: D 172 ASP cc_start: 0.7975 (m-30) cc_final: 0.7667 (m-30) REVERT: D 255 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.8024 (mtt90) REVERT: E 236 PHE cc_start: 0.7164 (m-80) cc_final: 0.6921 (m-80) REVERT: E 245 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.6567 (t80) outliers start: 32 outliers final: 24 residues processed: 178 average time/residue: 0.2404 time to fit residues: 60.8688 Evaluate side-chains 180 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 0.0040 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 139 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11585 Z= 0.177 Angle : 0.488 6.145 15790 Z= 0.243 Chirality : 0.046 0.131 1740 Planarity : 0.002 0.020 2005 Dihedral : 3.826 15.838 1510 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.50 % Allowed : 16.85 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1360 helix: 0.81 (0.26), residues: 425 sheet: 0.67 (0.27), residues: 405 loop : -1.92 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 PHE 0.008 0.001 PHE E 236 TYR 0.015 0.001 TYR C 245 ARG 0.003 0.000 ARG D 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.279 Fit side-chains REVERT: A 236 PHE cc_start: 0.7179 (m-80) cc_final: 0.6930 (m-80) REVERT: A 245 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.6880 (t80) REVERT: B 159 GLU cc_start: 0.7547 (pm20) cc_final: 0.7244 (pm20) REVERT: B 239 MET cc_start: 0.7160 (tpp) cc_final: 0.6865 (ttp) REVERT: B 245 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6918 (t80) REVERT: C 59 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 245 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.6937 (t80) REVERT: D 172 ASP cc_start: 0.7985 (m-30) cc_final: 0.7696 (m-30) REVERT: D 255 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8010 (mtt90) REVERT: E 245 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6429 (t80) outliers start: 31 outliers final: 25 residues processed: 175 average time/residue: 0.2322 time to fit residues: 58.5476 Evaluate side-chains 174 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 98 optimal weight: 0.0020 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 110 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 169 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117059 restraints weight = 12334.855| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.79 r_work: 0.3062 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11585 Z= 0.114 Angle : 0.464 7.055 15790 Z= 0.229 Chirality : 0.044 0.128 1740 Planarity : 0.002 0.019 2005 Dihedral : 3.557 14.234 1510 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.94 % Allowed : 17.42 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1360 helix: 0.88 (0.26), residues: 425 sheet: 1.31 (0.27), residues: 380 loop : -2.05 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 206 HIS 0.002 0.000 HIS B 177 PHE 0.009 0.001 PHE C 106 TYR 0.013 0.001 TYR E 245 ARG 0.003 0.000 ARG D 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.09 seconds wall clock time: 46 minutes 58.82 seconds (2818.82 seconds total)