Starting phenix.real_space_refine on Sat Dec 9 02:05:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsa_21373/12_2023/6vsa_21373.pdb" } resolution = 2.32 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= 0.020 sd= 0.129 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 50 5.16 5 C 6230 2.51 5 N 1610 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V GLU 31": "OE1" <-> "OE2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V GLU 162": "OE1" <-> "OE2" Residue "V GLU 215": "OE1" <-> "OE2" Residue "V PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 81": "OE1" <-> "OE2" Residue "W GLU 86": "OE1" <-> "OE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W GLU 215": "OE1" <-> "OE2" Residue "W PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 81": "OE1" <-> "OE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X ARG 128": "NH1" <-> "NH2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X GLU 227": "OE1" <-> "OE2" Residue "X PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 240": "OE1" <-> "OE2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y VAL 127": "CG1" <-> "CG2" Residue "Y ARG 129": "NH1" <-> "NH2" Residue "Y GLU 162": "OE1" <-> "OE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z GLU 126": "OE1" <-> "OE2" Residue "Z GLU 215": "OE1" <-> "OE2" Residue "Z PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9712 Number of models: 1 Model: "" Number of chains: 10 Chain: "V" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "W" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "X" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Y" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "Z" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1934 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "X" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 5.39, per 1000 atoms: 0.55 Number of scatterers: 9712 At special positions: 0 Unit cell: (97.2, 99.36, 76.32, 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 50 16.00 O 1822 8.00 N 1610 7.00 C 6230 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'V' and resid 21 through 28 Processing helix chain 'V' and resid 29 through 53 Processing helix chain 'V' and resid 78 through 91 Processing helix chain 'V' and resid 92 through 96 Processing helix chain 'V' and resid 124 through 132 Processing helix chain 'V' and resid 160 through 178 removed outlier: 3.534A pdb=" N ALA V 170 " --> pdb=" O GLU V 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR V 178 " --> pdb=" O THR V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 217 removed outlier: 3.804A pdb=" N LYS V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 225 Processing helix chain 'V' and resid 238 through 240 No H-bonds generated for 'chain 'V' and resid 238 through 240' Processing helix chain 'V' and resid 241 through 246 Processing helix chain 'W' and resid 21 through 28 Processing helix chain 'W' and resid 29 through 53 Processing helix chain 'W' and resid 78 through 91 Processing helix chain 'W' and resid 92 through 96 Processing helix chain 'W' and resid 124 through 132 Processing helix chain 'W' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA W 170 " --> pdb=" O GLU W 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR W 178 " --> pdb=" O THR W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 217 removed outlier: 3.806A pdb=" N LYS W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 225 Processing helix chain 'W' and resid 238 through 240 No H-bonds generated for 'chain 'W' and resid 238 through 240' Processing helix chain 'W' and resid 241 through 246 Processing helix chain 'X' and resid 21 through 28 Processing helix chain 'X' and resid 29 through 53 Processing helix chain 'X' and resid 78 through 91 Processing helix chain 'X' and resid 92 through 96 Processing helix chain 'X' and resid 124 through 132 Processing helix chain 'X' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA X 170 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR X 178 " --> pdb=" O THR X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 217 removed outlier: 3.808A pdb=" N LYS X 210 " --> pdb=" O ALA X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 225 Processing helix chain 'X' and resid 238 through 240 No H-bonds generated for 'chain 'X' and resid 238 through 240' Processing helix chain 'X' and resid 241 through 246 Processing helix chain 'Y' and resid 21 through 28 Processing helix chain 'Y' and resid 29 through 53 Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 92 through 96 Processing helix chain 'Y' and resid 124 through 132 removed outlier: 5.975A pdb=" N ARG Y 130 " --> pdb=" O GLU Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 178 removed outlier: 3.533A pdb=" N ALA Y 170 " --> pdb=" O GLU Y 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Y 178 " --> pdb=" O THR Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 removed outlier: 3.807A pdb=" N LYS Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 225 Processing helix chain 'Y' and resid 238 through 240 No H-bonds generated for 'chain 'Y' and resid 238 through 240' Processing helix chain 'Y' and resid 241 through 246 Processing helix chain 'Z' and resid 21 through 28 Processing helix chain 'Z' and resid 29 through 53 Processing helix chain 'Z' and resid 78 through 91 Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 124 through 132 Processing helix chain 'Z' and resid 160 through 178 removed outlier: 3.537A pdb=" N ALA Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR Z 178 " --> pdb=" O THR Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 217 removed outlier: 3.804A pdb=" N LYS Z 210 " --> pdb=" O ALA Z 206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 225 Processing helix chain 'Z' and resid 238 through 240 No H-bonds generated for 'chain 'Z' and resid 238 through 240' Processing helix chain 'Z' and resid 241 through 246 Processing sheet with id=AA1, first strand: chain 'V' and resid 226 through 228 removed outlier: 4.169A pdb=" N TRP V 11 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR V 19 " --> pdb=" O PRO V 100 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU V 109 " --> pdb=" O ILE V 186 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE V 186 " --> pdb=" O GLU V 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 150 through 151 Processing sheet with id=AA3, first strand: chain 'W' and resid 226 through 228 removed outlier: 5.929A pdb=" N ASP W 9 " --> pdb=" O LEU W 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU W 110 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP W 11 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR W 19 " --> pdb=" O PRO W 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU W 109 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE W 186 " --> pdb=" O GLU W 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'X' and resid 226 through 228 removed outlier: 5.945A pdb=" N ASP X 9 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU X 110 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP X 11 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR X 19 " --> pdb=" O PRO X 100 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU X 109 " --> pdb=" O ILE X 186 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE X 186 " --> pdb=" O GLU X 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 150 through 151 Processing sheet with id=AA7, first strand: chain 'Y' and resid 226 through 228 removed outlier: 5.950A pdb=" N ASP Y 9 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU Y 110 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP Y 11 " --> pdb=" O VAL Y 108 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR Y 19 " --> pdb=" O PRO Y 100 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 109 " --> pdb=" O ILE Y 186 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE Y 186 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'Z' and resid 226 through 228 removed outlier: 5.947A pdb=" N ASP Z 9 " --> pdb=" O LEU Z 110 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU Z 110 " --> pdb=" O ASP Z 9 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP Z 11 " --> pdb=" O VAL Z 108 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR Z 19 " --> pdb=" O PRO Z 100 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Z 109 " --> pdb=" O ILE Z 186 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE Z 186 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 150 through 151 569 hydrogen bonds defined for protein. 1572 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: 3.00 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2519 1.33 - 1.46: 3125 1.46 - 1.59: 4186 1.59 - 1.73: 0 1.73 - 1.86: 90 Bond restraints: 9920 Sorted by residual: bond pdb=" CA SER W 230 " pdb=" CB SER W 230 " ideal model delta sigma weight residual 1.529 1.435 0.094 1.58e-02 4.01e+03 3.57e+01 bond pdb=" CA SER X 230 " pdb=" CB SER X 230 " ideal model delta sigma weight residual 1.529 1.436 0.093 1.58e-02 4.01e+03 3.45e+01 bond pdb=" CA SER Z 230 " pdb=" CB SER Z 230 " ideal model delta sigma weight residual 1.529 1.436 0.093 1.58e-02 4.01e+03 3.44e+01 bond pdb=" CA SER Y 230 " pdb=" CB SER Y 230 " ideal model delta sigma weight residual 1.529 1.438 0.092 1.58e-02 4.01e+03 3.36e+01 bond pdb=" CA SER V 230 " pdb=" CB SER V 230 " ideal model delta sigma weight residual 1.529 1.439 0.090 1.58e-02 4.01e+03 3.25e+01 ... (remaining 9915 not shown) Histogram of bond angle deviations from ideal: 94.91 - 102.82: 169 102.82 - 110.73: 3272 110.73 - 118.65: 4556 118.65 - 126.56: 5268 126.56 - 134.47: 160 Bond angle restraints: 13425 Sorted by residual: angle pdb=" CA PRO V 121 " pdb=" N PRO V 121 " pdb=" CD PRO V 121 " ideal model delta sigma weight residual 112.00 99.12 12.88 1.40e+00 5.10e-01 8.47e+01 angle pdb=" CB GLU W 31 " pdb=" CG GLU W 31 " pdb=" CD GLU W 31 " ideal model delta sigma weight residual 112.60 127.26 -14.66 1.70e+00 3.46e-01 7.43e+01 angle pdb=" CB ARG Z 169 " pdb=" CG ARG Z 169 " pdb=" CD ARG Z 169 " ideal model delta sigma weight residual 111.30 130.39 -19.09 2.30e+00 1.89e-01 6.89e+01 angle pdb=" CA THR Y 19 " pdb=" CB THR Y 19 " pdb=" OG1 THR Y 19 " ideal model delta sigma weight residual 109.60 98.34 11.26 1.50e+00 4.44e-01 5.63e+01 angle pdb=" CG ARG X 164 " pdb=" CD ARG X 164 " pdb=" NE ARG X 164 " ideal model delta sigma weight residual 112.00 97.79 14.21 2.20e+00 2.07e-01 4.17e+01 ... (remaining 13420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 5006 18.08 - 36.15: 617 36.15 - 54.23: 175 54.23 - 72.31: 33 72.31 - 90.38: 19 Dihedral angle restraints: 5850 sinusoidal: 2405 harmonic: 3445 Sorted by residual: dihedral pdb=" C MET Z 146 " pdb=" N MET Z 146 " pdb=" CA MET Z 146 " pdb=" CB MET Z 146 " ideal model delta harmonic sigma weight residual -122.60 -103.03 -19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N MET Z 146 " pdb=" C MET Z 146 " pdb=" CA MET Z 146 " pdb=" CB MET Z 146 " ideal model delta harmonic sigma weight residual 122.80 104.77 18.03 0 2.50e+00 1.60e-01 5.20e+01 dihedral pdb=" C CYS X 142 " pdb=" N CYS X 142 " pdb=" CA CYS X 142 " pdb=" CB CYS X 142 " ideal model delta harmonic sigma weight residual -122.60 -106.68 -15.92 0 2.50e+00 1.60e-01 4.05e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.555: 1428 0.555 - 1.111: 1 1.111 - 1.666: 0 1.666 - 2.221: 0 2.221 - 2.777: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CB VAL Y 127 " pdb=" CA VAL Y 127 " pdb=" CG1 VAL Y 127 " pdb=" CG2 VAL Y 127 " both_signs ideal model delta sigma weight residual False -2.63 0.15 -2.78 2.00e-01 2.50e+01 1.93e+02 chirality pdb=" CA GLU W 31 " pdb=" N GLU W 31 " pdb=" C GLU W 31 " pdb=" CB GLU W 31 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA MET Z 146 " pdb=" N MET Z 146 " pdb=" C MET Z 146 " pdb=" CB MET Z 146 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.51 2.00e-01 2.50e+01 6.63e+00 ... (remaining 1427 not shown) Planarity restraints: 1705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 178 " -0.040 2.00e-02 2.50e+03 8.18e-02 6.70e+01 pdb=" C TYR Y 178 " 0.142 2.00e-02 2.50e+03 pdb=" O TYR Y 178 " -0.053 2.00e-02 2.50e+03 pdb=" N ALA Y 179 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 225 " 0.012 2.00e-02 2.50e+03 4.14e-02 3.00e+01 pdb=" CG PHE Z 225 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 225 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 225 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE Z 225 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 225 " 0.011 2.00e-02 2.50e+03 4.12e-02 2.96e+01 pdb=" CG PHE V 225 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE V 225 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE V 225 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE V 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE V 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE V 225 " 0.078 2.00e-02 2.50e+03 ... (remaining 1702 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 245 2.62 - 3.19: 8760 3.19 - 3.76: 17303 3.76 - 4.33: 25745 4.33 - 4.90: 39699 Nonbonded interactions: 91752 Sorted by model distance: nonbonded pdb=" NZ LYS W 67 " pdb=" OD1 ASP Y 194 " model vdw 2.048 2.520 nonbonded pdb=" NZ LYS X 67 " pdb=" OD1 ASP Z 194 " model vdw 2.054 2.520 nonbonded pdb=" OD1 ASP X 194 " pdb=" NZ LYS Y 67 " model vdw 2.066 2.520 nonbonded pdb=" OD1 ASP V 194 " pdb=" NZ LYS Z 67 " model vdw 2.073 2.520 nonbonded pdb=" O GLY Y 65 " pdb=" O HOH Y 301 " model vdw 2.073 2.440 ... (remaining 91747 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 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 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: 1.760 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: 4.030 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.100 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 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 : 0.013 0.115 9920 Z= 0.861 Angle : 2.263 19.087 13425 Z= 1.465 Chirality : 0.159 2.777 1430 Planarity : 0.012 0.082 1705 Dihedral : 18.035 90.385 3630 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.44 % Allowed : 13.04 % Favored : 82.51 % Cbeta Deviations : 6.76 % 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: -1.58 (0.22), residues: 1155 helix: -1.92 (0.19), residues: 505 sheet: 0.61 (0.28), residues: 315 loop : -0.88 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.014 TRP W 25 HIS 0.030 0.008 HIS W 15 PHE 0.079 0.014 PHE Z 225 TYR 0.049 0.011 TYR X 157 ARG 0.038 0.004 ARG Y 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 101 time to evaluate : 1.252 Fit side-chains outliers start: 46 outliers final: 5 residues processed: 134 average time/residue: 1.5258 time to fit residues: 216.9176 Evaluate side-chains 77 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 83 HIS W 163 GLN ** W 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9920 Z= 0.213 Angle : 0.585 7.196 13425 Z= 0.313 Chirality : 0.042 0.297 1430 Planarity : 0.004 0.036 1705 Dihedral : 4.985 20.289 1300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 2.22 % Allowed : 16.52 % Favored : 81.26 % 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: -0.10 (0.23), residues: 1155 helix: 0.28 (0.21), residues: 510 sheet: -0.28 (0.25), residues: 360 loop : 0.06 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 156 HIS 0.002 0.001 HIS V 83 PHE 0.015 0.001 PHE Y 225 TYR 0.017 0.002 TYR W 157 ARG 0.007 0.001 ARG Y 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.361 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 117 average time/residue: 1.3908 time to fit residues: 174.2272 Evaluate side-chains 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.5585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 163 GLN Y 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9920 Z= 0.281 Angle : 0.539 6.453 13425 Z= 0.287 Chirality : 0.042 0.383 1430 Planarity : 0.004 0.031 1705 Dihedral : 4.679 19.456 1300 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Rotamer: Outliers : 2.51 % Allowed : 17.29 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1155 helix: 0.89 (0.22), residues: 520 sheet: -0.35 (0.26), residues: 365 loop : 0.46 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 156 HIS 0.002 0.001 HIS Y 83 PHE 0.012 0.001 PHE Z 143 TYR 0.016 0.002 TYR W 157 ARG 0.004 0.000 ARG Y 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 1.076 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 101 average time/residue: 1.3752 time to fit residues: 148.8490 Evaluate side-chains 95 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1353 time to fit residues: 2.1491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9920 Z= 0.271 Angle : 0.521 7.155 13425 Z= 0.273 Chirality : 0.041 0.312 1430 Planarity : 0.004 0.031 1705 Dihedral : 4.553 18.792 1300 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.61 % Favored : 99.31 % Rotamer: Outliers : 3.38 % Allowed : 16.33 % Favored : 80.29 % 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: 0.55 (0.24), residues: 1155 helix: 0.96 (0.22), residues: 535 sheet: -0.21 (0.27), residues: 345 loop : 0.37 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 156 HIS 0.002 0.001 HIS W 171 PHE 0.011 0.001 PHE Z 143 TYR 0.015 0.002 TYR Y 157 ARG 0.005 0.000 ARG X 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 76 time to evaluate : 1.199 Fit side-chains outliers start: 35 outliers final: 20 residues processed: 107 average time/residue: 1.2502 time to fit residues: 143.8659 Evaluate side-chains 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 0.1501 time to fit residues: 1.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 241 ASN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9920 Z= 0.340 Angle : 0.543 7.480 13425 Z= 0.284 Chirality : 0.042 0.370 1430 Planarity : 0.004 0.032 1705 Dihedral : 4.574 18.883 1300 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Rotamer: Outliers : 3.29 % Allowed : 16.62 % Favored : 80.10 % 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: 1.04 (0.25), residues: 1155 helix: 1.37 (0.22), residues: 510 sheet: -0.33 (0.27), residues: 345 loop : 1.16 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 156 HIS 0.003 0.001 HIS W 171 PHE 0.012 0.001 PHE Z 225 TYR 0.016 0.002 TYR W 157 ARG 0.003 0.000 ARG X 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 1.199 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 102 average time/residue: 1.4989 time to fit residues: 163.2948 Evaluate side-chains 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.9963 time to fit residues: 3.7879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9920 Z= 0.192 Angle : 0.497 8.054 13425 Z= 0.256 Chirality : 0.040 0.309 1430 Planarity : 0.003 0.032 1705 Dihedral : 4.364 18.241 1300 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 3.00 % Allowed : 17.00 % Favored : 80.00 % 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: 0.79 (0.24), residues: 1155 helix: 1.19 (0.22), residues: 540 sheet: -0.33 (0.27), residues: 345 loop : 0.74 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.011 0.001 PHE Z 225 TYR 0.012 0.001 TYR X 97 ARG 0.003 0.000 ARG V 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 1.092 Fit side-chains outliers start: 31 outliers final: 20 residues processed: 101 average time/residue: 1.2464 time to fit residues: 136.1808 Evaluate side-chains 91 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.1306 time to fit residues: 2.1723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 110 optimal weight: 0.0770 chunk 69 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 163 GLN ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9920 Z= 0.190 Angle : 0.491 7.920 13425 Z= 0.253 Chirality : 0.040 0.356 1430 Planarity : 0.003 0.033 1705 Dihedral : 4.274 17.724 1300 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 2.32 % Allowed : 17.68 % Favored : 80.00 % 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: 1.32 (0.25), residues: 1155 helix: 1.66 (0.22), residues: 510 sheet: -0.37 (0.27), residues: 345 loop : 1.46 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 156 HIS 0.002 0.001 HIS V 83 PHE 0.010 0.001 PHE Z 225 TYR 0.012 0.001 TYR Z 97 ARG 0.003 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.201 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 98 average time/residue: 1.2573 time to fit residues: 132.9179 Evaluate side-chains 95 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.1723 time to fit residues: 2.0605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9920 Z= 0.224 Angle : 0.510 8.807 13425 Z= 0.261 Chirality : 0.040 0.330 1430 Planarity : 0.003 0.033 1705 Dihedral : 4.276 17.479 1300 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 2.32 % Allowed : 17.87 % Favored : 79.81 % 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: 1.29 (0.24), residues: 1155 helix: 1.66 (0.22), residues: 510 sheet: -0.47 (0.26), residues: 345 loop : 1.50 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 156 HIS 0.002 0.001 HIS V 83 PHE 0.011 0.001 PHE X 225 TYR 0.013 0.001 TYR V 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.108 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 96 average time/residue: 1.2895 time to fit residues: 133.3015 Evaluate side-chains 92 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.9257 time to fit residues: 3.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 62 optimal weight: 0.0370 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9920 Z= 0.244 Angle : 0.515 8.620 13425 Z= 0.265 Chirality : 0.041 0.322 1430 Planarity : 0.003 0.033 1705 Dihedral : 4.295 17.362 1300 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 2.22 % Allowed : 17.87 % Favored : 79.90 % 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: 1.22 (0.24), residues: 1155 helix: 1.63 (0.22), residues: 510 sheet: -0.57 (0.26), residues: 345 loop : 1.49 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.011 0.001 PHE Z 225 TYR 0.013 0.001 TYR V 97 ARG 0.002 0.000 ARG Z 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 1.113 Fit side-chains outliers start: 23 outliers final: 20 residues processed: 94 average time/residue: 1.2802 time to fit residues: 129.5063 Evaluate side-chains 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.1647 time to fit residues: 2.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9920 Z= 0.198 Angle : 0.510 9.409 13425 Z= 0.259 Chirality : 0.040 0.313 1430 Planarity : 0.003 0.033 1705 Dihedral : 4.214 17.174 1300 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 1.84 % Allowed : 18.16 % Favored : 80.00 % 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: 1.24 (0.24), residues: 1155 helix: 1.66 (0.22), residues: 510 sheet: -0.59 (0.26), residues: 345 loop : 1.51 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.010 0.001 PHE Z 225 TYR 0.012 0.001 TYR V 97 ARG 0.002 0.000 ARG Z 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.126 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 1.3075 time to fit residues: 133.7775 Evaluate side-chains 89 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.0898 time to fit residues: 1.7618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0020 chunk 80 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.061651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050617 restraints weight = 35472.787| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.75 r_work: 0.2959 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9920 Z= 0.241 Angle : 0.515 8.650 13425 Z= 0.265 Chirality : 0.041 0.332 1430 Planarity : 0.003 0.033 1705 Dihedral : 4.256 17.334 1300 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Rotamer: Outliers : 1.74 % Allowed : 18.55 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1155 helix: 1.61 (0.22), residues: 510 sheet: -0.67 (0.26), residues: 345 loop : 1.50 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 156 HIS 0.002 0.001 HIS Z 83 PHE 0.010 0.001 PHE Z 225 TYR 0.013 0.001 TYR V 97 ARG 0.002 0.000 ARG Z 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.59 seconds wall clock time: 57 minutes 35.92 seconds (3455.92 seconds total)