Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:18:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/04_2023/6vsc_21376.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/04_2023/6vsc_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_21376/04_2023/6vsc_21376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/04_2023/6vsc_21376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/04_2023/6vsc_21376.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/04_2023/6vsc_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 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 1780 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 "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-1.21rc1-4938/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: 5.62, per 1000 atoms: 0.58 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 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: 4.60 Conformation dependent library (CDL) restraints added in 1.5 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: 0.69 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: 3.13 Time building geometry restraints manager: 4.91 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 4.230 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.510 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 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 : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 12 residues processed: 405 average time/residue: 1.2925 time to fit residues: 555.7710 Evaluate side-chains 265 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0892 time to fit residues: 1.6124 ------------------------------------------------------------------------------- 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8751 moved from start: 0.3462 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= 0.244 Angle : 0.655 7.719 13425 Z= 0.344 Chirality : 0.044 0.192 1430 Planarity : 0.005 0.038 1705 Dihedral : 5.146 22.232 1300 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.72 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: -0.39 (0.23), residues: 1155 helix: 0.03 (0.22), residues: 535 sheet: 0.15 (0.28), residues: 320 loop : -0.91 (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 388 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 332 time to evaluate : 1.231 Fit side-chains outliers start: 56 outliers final: 16 residues processed: 366 average time/residue: 1.1216 time to fit residues: 441.0114 Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 283 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 5 average time/residue: 0.3103 time to fit residues: 3.4485 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8763 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 9920 Z= 0.291 Angle : 0.643 7.486 13425 Z= 0.328 Chirality : 0.044 0.286 1430 Planarity : 0.005 0.061 1705 Dihedral : 4.817 21.547 1300 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 5.12 % 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: 0.09 (0.24), residues: 1155 helix: 0.51 (0.22), residues: 540 sheet: 0.09 (0.27), residues: 325 loop : -0.51 (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 344 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 291 time to evaluate : 1.181 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 321 average time/residue: 1.1776 time to fit residues: 404.8491 Evaluate side-chains 304 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 10 average time/residue: 0.2679 time to fit residues: 5.0035 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 247 HIS Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 9920 Z= 0.303 Angle : 0.630 8.110 13425 Z= 0.318 Chirality : 0.043 0.195 1430 Planarity : 0.005 0.051 1705 Dihedral : 4.704 21.762 1300 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % 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: 0.13 (0.24), residues: 1155 helix: 0.62 (0.22), residues: 535 sheet: -0.10 (0.26), residues: 325 loop : -0.36 (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 331 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 276 time to evaluate : 1.080 Fit side-chains outliers start: 55 outliers final: 27 residues processed: 310 average time/residue: 1.2160 time to fit residues: 403.0774 Evaluate side-chains 289 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 9 average time/residue: 0.2958 time to fit residues: 4.9516 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4204 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= 0.263 Angle : 0.618 7.867 13425 Z= 0.312 Chirality : 0.043 0.147 1430 Planarity : 0.005 0.043 1705 Dihedral : 4.603 21.614 1300 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % 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 (0.24), residues: 1155 helix: 0.60 (0.22), residues: 540 sheet: -0.16 (0.26), residues: 305 loop : 0.09 (0.35), 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 342 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 288 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 320 average time/residue: 1.1860 time to fit residues: 406.2279 Evaluate side-chains 293 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 265 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.6134 time to fit residues: 5.7336 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 Z 15 HIS Z 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4335 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= 0.283 Angle : 0.647 9.386 13425 Z= 0.321 Chirality : 0.043 0.162 1430 Planarity : 0.005 0.042 1705 Dihedral : 4.612 20.690 1300 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Rotamer Outliers : 5.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1155 helix: 0.60 (0.22), residues: 540 sheet: -0.35 (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 335 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 274 time to evaluate : 1.101 Fit side-chains outliers start: 61 outliers final: 38 residues processed: 316 average time/residue: 1.2011 time to fit residues: 406.0496 Evaluate side-chains 304 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 30 residues processed: 10 average time/residue: 0.3125 time to fit residues: 5.5316 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.4463 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= 0.245 Angle : 0.650 10.479 13425 Z= 0.321 Chirality : 0.044 0.160 1430 Planarity : 0.005 0.048 1705 Dihedral : 4.575 21.711 1300 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer Outliers : 5.12 % 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: 0.61 (0.22), residues: 540 sheet: -0.43 (0.25), residues: 305 loop : 0.22 (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 329 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 1.176 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 35 residues processed: 316 average time/residue: 1.2308 time to fit residues: 416.3415 Evaluate side-chains 306 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 5 average time/residue: 0.1756 time to fit residues: 2.7513 ------------------------------------------------------------------------------- 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: 0.6980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9920 Z= 0.235 Angle : 0.653 9.419 13425 Z= 0.322 Chirality : 0.044 0.187 1430 Planarity : 0.005 0.053 1705 Dihedral : 4.538 20.562 1300 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % Rotamer Outliers : 4.35 % 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: 0.64 (0.22), residues: 540 sheet: -0.44 (0.25), residues: 305 loop : 0.26 (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: 45 poor density : 273 time to evaluate : 1.180 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 34 residues processed: 310 average time/residue: 1.2137 time to fit residues: 402.2498 Evaluate side-chains 301 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 3 average time/residue: 0.6765 time to fit residues: 3.7328 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4475 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= 0.313 Angle : 0.695 10.225 13425 Z= 0.344 Chirality : 0.045 0.207 1430 Planarity : 0.005 0.053 1705 Dihedral : 4.666 21.498 1300 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % 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: 0.15 (0.23), residues: 1155 helix: 0.59 (0.22), residues: 540 sheet: -0.49 (0.25), residues: 305 loop : 0.23 (0.34), residues: 310 *********************** 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 308 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 262 time to evaluate : 1.200 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 41 residues processed: 298 average time/residue: 1.2230 time to fit residues: 389.6087 Evaluate side-chains 297 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 34 residues processed: 8 average time/residue: 0.1751 time to fit residues: 3.5348 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4738 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= 0.203 Angle : 0.665 9.535 13425 Z= 0.326 Chirality : 0.044 0.164 1430 Planarity : 0.005 0.056 1705 Dihedral : 4.569 20.864 1300 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.56 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: 0.19 (0.23), residues: 1155 helix: 0.67 (0.22), residues: 540 sheet: -0.46 (0.25), residues: 325 loop : 0.22 (0.35), residues: 290 ********************** 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 320 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 1.200 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 32 residues processed: 317 average time/residue: 1.1871 time to fit residues: 402.7390 Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 2 average time/residue: 0.2252 time to fit residues: 2.2661 ------------------------------------------------------------------------------- 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: 0.8980 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 30 ASN Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096418 restraints weight = 20290.946| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.31 r_work: 0.3403 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4781 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= 0.222 Angle : 0.685 10.416 13425 Z= 0.337 Chirality : 0.046 0.353 1430 Planarity : 0.005 0.057 1705 Dihedral : 4.579 21.974 1300 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % 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: 0.71 (0.24), residues: 1155 helix: 0.98 (0.22), residues: 515 sheet: -0.41 (0.25), residues: 305 loop : 0.92 (0.36), residues: 335 =============================================================================== Job complete usr+sys time: 5855.12 seconds wall clock time: 103 minutes 38.23 seconds (6218.23 seconds total)