Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 22:24:11 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/12_2021/6vsc_21376.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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 "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 "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 GLU 240": "OE1" <-> "OE2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y ARG 129": "NH1" <-> "NH2" Residue "Y GLU 162": "OE1" <-> "OE2" Residue "Y GLU 215": "OE1" <-> "OE2" 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 GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9670 Number of models: 1 Model: "" Number of chains: 5 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 Time building chain proxies: 6.44, per 1000 atoms: 0.67 Number of scatterers: 9670 At special positions: 0 Unit cell: (101.01, 98.28, 76.44, 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 1780 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 Amimo 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: 4.27 Conformation dependent library (CDL) restraints added in 1.7 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: 0.66 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: 3.615A pdb=" N ALA V 170 " --> pdb=" O GLU V 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR V 178 " --> pdb=" O THR V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 217 removed outlier: 3.786A 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: 3.616A pdb=" N ALA W 170 " --> pdb=" O GLU W 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS W 171 " --> pdb=" O LEU W 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR W 178 " --> pdb=" O THR W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 217 removed outlier: 3.784A 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: 3.615A pdb=" N ALA X 170 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS X 171 " --> pdb=" O LEU X 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR X 178 " --> pdb=" O THR X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 217 removed outlier: 3.782A 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: 6.025A pdb=" N ARG Y 130 " --> pdb=" O GLU Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 178 removed outlier: 3.612A pdb=" N ALA Y 170 " --> pdb=" O GLU Y 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR Y 178 " --> pdb=" O THR Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 removed outlier: 3.779A 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: 3.617A pdb=" N ALA Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS Z 171 " --> pdb=" O LEU Z 167 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Z 178 " --> pdb=" O THR Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 217 removed outlier: 3.785A 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: 4.168A pdb=" N TRP V 11 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR V 19 " --> pdb=" O PRO V 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU V 109 " --> pdb=" O ILE V 186 " (cutoff:3.500A) removed outlier: 5.600A 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: 5.941A pdb=" N ASP W 9 " --> pdb=" O LEU W 110 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU W 110 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP W 11 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR W 19 " --> pdb=" O PRO W 100 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU W 109 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.595A 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: 5.937A pdb=" N ASP X 9 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU X 110 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TRP X 11 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR X 19 " --> pdb=" O PRO X 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU X 109 " --> pdb=" O ILE X 186 " (cutoff:3.500A) removed outlier: 5.601A 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: 5.941A pdb=" N ASP Y 9 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU Y 110 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP Y 11 " --> pdb=" O VAL Y 108 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR Y 19 " --> pdb=" O PRO Y 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU Y 109 " --> pdb=" O ILE Y 186 " (cutoff:3.500A) removed outlier: 5.595A 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: 5.937A pdb=" N ASP Z 9 " --> pdb=" O LEU Z 110 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU Z 110 " --> pdb=" O ASP Z 9 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP Z 11 " --> pdb=" O VAL Z 108 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR Z 19 " --> pdb=" O PRO Z 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU Z 109 " --> pdb=" O ILE Z 186 " (cutoff:3.500A) removed outlier: 5.586A 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 151 564 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2284 1.33 - 1.47: 3464 1.47 - 1.62: 4082 1.62 - 1.76: 5 1.76 - 1.90: 85 Bond restraints: 9920 Sorted by residual: bond pdb=" CE1 HIS Z 83 " pdb=" NE2 HIS Z 83 " ideal model delta sigma weight residual 1.321 1.389 -0.068 1.00e-02 1.00e+04 4.66e+01 bond pdb=" CE1 HIS X 83 " pdb=" NE2 HIS X 83 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" CE1 HIS Y 83 " pdb=" NE2 HIS Y 83 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.29e+01 bond pdb=" CE1 HIS V 83 " pdb=" NE2 HIS V 83 " ideal model delta sigma weight residual 1.321 1.385 -0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" CE1 HIS W 83 " pdb=" NE2 HIS W 83 " ideal model delta sigma weight residual 1.321 1.382 -0.061 1.00e-02 1.00e+04 3.66e+01 ... (remaining 9915 not shown) Histogram of bond angle deviations from ideal: 94.24 - 102.33: 141 102.33 - 110.42: 3085 110.42 - 118.50: 4809 118.50 - 126.59: 5205 126.59 - 134.68: 185 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 99.20 12.80 1.40e+00 5.10e-01 8.36e+01 angle pdb=" CG ARG Y 164 " pdb=" CD ARG Y 164 " pdb=" NE ARG Y 164 " ideal model delta sigma weight residual 112.00 94.97 17.03 2.20e+00 2.07e-01 5.99e+01 angle pdb=" CG ARG W 164 " pdb=" CD ARG W 164 " pdb=" NE ARG W 164 " ideal model delta sigma weight residual 112.00 95.09 16.91 2.20e+00 2.07e-01 5.91e+01 angle pdb=" CG ARG V 164 " pdb=" CD ARG V 164 " pdb=" NE ARG V 164 " ideal model delta sigma weight residual 112.00 95.18 16.82 2.20e+00 2.07e-01 5.85e+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 95.22 16.78 2.20e+00 2.07e-01 5.82e+01 ... (remaining 13420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4897 17.82 - 35.64: 713 35.64 - 53.45: 174 53.45 - 71.27: 52 71.27 - 89.09: 14 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 -102.00 -20.60 0 2.50e+00 1.60e-01 6.79e+01 dihedral pdb=" C VAL Z 221 " pdb=" N VAL Z 221 " pdb=" CA VAL Z 221 " pdb=" CB VAL Z 221 " ideal model delta harmonic sigma weight residual -122.00 -142.46 20.46 0 2.50e+00 1.60e-01 6.69e+01 dihedral pdb=" N VAL Z 221 " pdb=" C VAL Z 221 " pdb=" CA VAL Z 221 " pdb=" CB VAL Z 221 " ideal model delta harmonic sigma weight residual 123.40 143.85 -20.45 0 2.50e+00 1.60e-01 6.69e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1099 0.161 - 0.321: 272 0.321 - 0.482: 52 0.482 - 0.642: 1 0.642 - 0.803: 6 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA VAL Z 221 " pdb=" N VAL Z 221 " pdb=" C VAL Z 221 " pdb=" CB VAL Z 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA VAL X 221 " pdb=" N VAL X 221 " pdb=" C VAL X 221 " pdb=" CB VAL X 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA VAL V 221 " pdb=" N VAL V 221 " pdb=" C VAL V 221 " pdb=" CB VAL V 221 " both_signs ideal model delta sigma weight residual False 2.44 1.64 0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 1427 not shown) Planarity restraints: 1705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 178 " 0.030 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C TYR Y 178 " -0.106 2.00e-02 2.50e+03 pdb=" O TYR Y 178 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA Y 179 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 225 " -0.035 2.00e-02 2.50e+03 4.59e-02 3.69e+01 pdb=" CG PHE Z 225 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 225 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 225 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 225 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 225 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE Z 225 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 225 " 0.035 2.00e-02 2.50e+03 4.58e-02 3.67e+01 pdb=" CG PHE W 225 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE W 225 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE W 225 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE W 225 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE W 225 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE W 225 " 0.088 2.00e-02 2.50e+03 ... (remaining 1702 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 986 2.70 - 3.25: 9413 3.25 - 3.80: 18076 3.80 - 4.35: 24730 4.35 - 4.90: 38445 Nonbonded interactions: 91650 Sorted by model distance: nonbonded pdb=" NZ LYS V 67 " pdb=" OD1 ASP W 194 " model vdw 2.153 2.520 nonbonded pdb=" NZ LYS W 67 " pdb=" OD1 ASP Y 194 " model vdw 2.155 2.520 nonbonded pdb=" NZ LYS X 67 " pdb=" OD1 ASP Z 194 " model vdw 2.157 2.520 nonbonded pdb=" OD1 ASP X 194 " pdb=" NZ LYS Y 67 " model vdw 2.166 2.520 nonbonded pdb=" OD1 ASP V 194 " pdb=" NZ LYS Z 67 " model vdw 2.186 2.520 ... (remaining 91645 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 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 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Write .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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 29.780 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:11.800 Set ADP refinement strategy: 0.010 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 47.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 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 : 0.014 0.126 9920 Z= 0.903 Angle : 2.410 17.031 13425 Z= 1.576 Chirality : 0.153 0.803 1430 Planarity : 0.012 0.061 1705 Dihedral : 18.437 89.087 3630 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 7.73 % 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: -1.96 (0.23), residues: 1155 helix: -2.12 (0.18), residues: 510 sheet: 0.21 (0.29), residues: 320 loop : -1.01 (0.32), residues: 325 *********************** 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 433 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 353 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 12 residues processed: 405 average time/residue: 1.2194 time to fit residues: 526.1852 Evaluate side-chains 265 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0877 time to fit residues: 1.7895 ------------------------------------------------------------------------------- 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: 0.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 151 GLN V 247 HIS W 247 HIS X 55 GLN X 247 HIS ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 HIS Z 30 ASN Z 55 GLN Z 151 GLN Z 247 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9920 Z= 0.239 Angle : 0.648 7.988 13425 Z= 0.340 Chirality : 0.044 0.195 1430 Planarity : 0.005 0.040 1705 Dihedral : 5.137 22.036 1300 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer Outliers : 5.41 % 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: -0.37 (0.23), residues: 1155 helix: 0.03 (0.22), residues: 535 sheet: 0.16 (0.28), residues: 320 loop : -0.86 (0.32), residues: 300 *********************** 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 389 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 333 time to evaluate : 1.220 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 16 residues processed: 367 average time/residue: 1.0532 time to fit residues: 416.3405 Evaluate side-chains 301 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 4 average time/residue: 0.3886 time to fit residues: 3.4984 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 171 HIS V 247 HIS W 6 GLN X 171 HIS X 247 HIS Y 171 HIS Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9920 Z= 0.301 Angle : 0.645 7.574 13425 Z= 0.328 Chirality : 0.044 0.281 1430 Planarity : 0.005 0.044 1705 Dihedral : 4.799 21.491 1300 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer Outliers : 5.51 % 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: 0.07 (0.24), residues: 1155 helix: 0.53 (0.22), residues: 540 sheet: 0.06 (0.27), residues: 325 loop : -0.55 (0.35), residues: 290 *********************** 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 339 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 282 time to evaluate : 1.221 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 32 residues processed: 314 average time/residue: 1.0830 time to fit residues: 366.2024 Evaluate side-chains 296 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 13 average time/residue: 0.3519 time to fit residues: 7.1533 ------------------------------------------------------------------------------- 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: 7.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 247 HIS X 55 GLN X 241 ASN X 247 HIS Z 30 ASN Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9920 Z= 0.209 Angle : 0.602 7.603 13425 Z= 0.301 Chirality : 0.043 0.193 1430 Planarity : 0.004 0.044 1705 Dihedral : 4.574 22.157 1300 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer Outliers : 4.93 % 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: 0.21 (0.24), residues: 1155 helix: 0.66 (0.22), residues: 535 sheet: -0.08 (0.26), residues: 325 loop : -0.25 (0.35), residues: 295 *********************** 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 347 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 327 average time/residue: 1.1087 time to fit residues: 390.0352 Evaluate side-chains 298 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.5941 time to fit residues: 4.8241 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS W 83 HIS X 241 ASN X 247 HIS Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 9920 Z= 0.385 Angle : 0.670 9.997 13425 Z= 0.337 Chirality : 0.044 0.156 1430 Planarity : 0.005 0.041 1705 Dihedral : 4.670 20.872 1300 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Rotamer Outliers : 5.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1155 helix: 0.60 (0.22), residues: 540 sheet: -0.24 (0.26), residues: 305 loop : 0.03 (0.34), residues: 310 *********************** 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 319 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 1.319 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 36 residues processed: 300 average time/residue: 1.1408 time to fit residues: 366.9998 Evaluate side-chains 290 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 25 residues processed: 13 average time/residue: 0.4914 time to fit residues: 9.0753 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 55 GLN X 247 HIS Z 30 ASN Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9920 Z= 0.239 Angle : 0.623 9.415 13425 Z= 0.310 Chirality : 0.043 0.137 1430 Planarity : 0.005 0.044 1705 Dihedral : 4.526 21.842 1300 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 5.41 % 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: 0.21 (0.23), residues: 1155 helix: 0.63 (0.22), residues: 540 sheet: -0.36 (0.25), residues: 305 loop : 0.18 (0.34), residues: 310 *********************** 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 339 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 283 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 35 residues processed: 322 average time/residue: 0.9408 time to fit residues: 328.9278 Evaluate side-chains 306 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 29 residues processed: 7 average time/residue: 0.6330 time to fit residues: 6.7536 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 0.0070 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 241 ASN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9920 Z= 0.212 Angle : 0.635 10.067 13425 Z= 0.312 Chirality : 0.043 0.160 1430 Planarity : 0.005 0.049 1705 Dihedral : 4.438 20.473 1300 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1155 helix: 0.63 (0.22), residues: 540 sheet: -0.39 (0.25), residues: 305 loop : 0.30 (0.34), residues: 310 *********************** 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 331 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 277 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 41 residues processed: 315 average time/residue: 1.1143 time to fit residues: 377.5215 Evaluate side-chains 304 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 32 residues processed: 10 average time/residue: 0.4383 time to fit residues: 6.8591 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 241 ASN Z 30 ASN Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9920 Z= 0.257 Angle : 0.659 9.616 13425 Z= 0.324 Chirality : 0.043 0.194 1430 Planarity : 0.005 0.052 1705 Dihedral : 4.493 22.170 1300 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 4.73 % 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: 0.23 (0.23), residues: 1155 helix: 0.64 (0.22), residues: 540 sheet: -0.45 (0.25), residues: 305 loop : 0.32 (0.34), residues: 310 *********************** 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 318 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 36 residues processed: 307 average time/residue: 1.1015 time to fit residues: 363.6364 Evaluate side-chains 295 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 8 average time/residue: 0.4934 time to fit residues: 6.1485 ------------------------------------------------------------------------------- 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: 0.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 55 GLN X 241 ASN Z 15 HIS Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4517 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= 0.272 Angle : 0.682 10.267 13425 Z= 0.335 Chirality : 0.044 0.193 1430 Planarity : 0.005 0.053 1705 Dihedral : 4.544 20.861 1300 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 4.44 % 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: 0.18 (0.23), residues: 1155 helix: 0.62 (0.22), residues: 545 sheet: -0.50 (0.25), residues: 305 loop : 0.27 (0.34), residues: 305 *********************** 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 317 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 38 residues processed: 306 average time/residue: 1.1210 time to fit residues: 368.3829 Evaluate side-chains 302 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 8 average time/residue: 0.4798 time to fit residues: 6.1136 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS X 241 ASN Z 30 ASN Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9920 Z= 0.224 Angle : 0.680 10.510 13425 Z= 0.333 Chirality : 0.044 0.174 1430 Planarity : 0.005 0.059 1705 Dihedral : 4.528 21.455 1300 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1155 helix: 0.59 (0.22), residues: 540 sheet: -0.46 (0.25), residues: 305 loop : 0.36 (0.33), residues: 310 ********************** 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 312 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 275 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 32 residues processed: 307 average time/residue: 1.1050 time to fit residues: 364.1443 Evaluate side-chains 300 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.1736 time to fit residues: 2.4145 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 30 ASN V 241 ASN V 247 HIS ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.108969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096327 restraints weight = 19207.194| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.12 r_work: 0.3507 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3481 rms_B_bonded: 1.92 restraints_weight: 0.1250 r_work: 0.3468 rms_B_bonded: 2.02 restraints_weight: 0.0625 r_work: 0.3454 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3439 rms_B_bonded: 2.32 restraints_weight: 0.0156 r_work: 0.3423 rms_B_bonded: 2.52 restraints_weight: 0.0078 r_work: 0.3406 rms_B_bonded: 2.76 restraints_weight: 0.0039 r_work: 0.3387 rms_B_bonded: 3.05 restraints_weight: 0.0020 r_work: 0.3368 rms_B_bonded: 3.37 restraints_weight: 0.0010 r_work: 0.3347 rms_B_bonded: 3.75 restraints_weight: 0.0005 r_work: 0.3324 rms_B_bonded: 4.18 restraints_weight: 0.0002 r_work: 0.3299 rms_B_bonded: 4.66 restraints_weight: 0.0001 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9920 Z= 0.217 Angle : 0.673 9.700 13425 Z= 0.332 Chirality : 0.045 0.394 1430 Planarity : 0.005 0.064 1705 Dihedral : 4.552 23.373 1300 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer Outliers : 3.67 % 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: 0.63 (0.24), residues: 1155 helix: 0.89 (0.22), residues: 510 sheet: -0.44 (0.25), residues: 305 loop : 0.91 (0.35), residues: 340 =============================================================================== Job complete usr+sys time: 5293.81 seconds wall clock time: 96 minutes 6.08 seconds (5766.08 seconds total)