Starting phenix.real_space_refine on Thu Mar 14 20:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/03_2024/6vsc_21376.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/03_2024/6vsc_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_21376/03_2024/6vsc_21376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/03_2024/6vsc_21376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/03_2024/6vsc_21376.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsc_21376/03_2024/6vsc_21376.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.111 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-dev-5265/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: 5.64, 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: 3.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 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: 2.86 Time building geometry restraints manager: 4.23 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: 0.700 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: 3.800 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.200 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- 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 % Allowed : 11.59 % Favored : 80.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.012 TRP W 25 HIS 0.018 0.007 HIS W 58 PHE 0.088 0.016 PHE Z 225 TYR 0.053 0.011 TYR X 140 ARG 0.030 0.005 ARG Y 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 353 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8897 (tm-30) REVERT: V 109 GLU cc_start: 0.8648 (pt0) cc_final: 0.8330 (pm20) REVERT: V 110 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6810 (mp) REVERT: V 130 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8244 (ttp-170) REVERT: V 147 ASP cc_start: 0.9198 (m-30) cc_final: 0.8951 (m-30) REVERT: V 153 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7276 (p0) REVERT: V 181 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8024 (mmtm) REVERT: V 184 GLN cc_start: 0.9078 (tt0) cc_final: 0.8779 (pm20) REVERT: V 196 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8965 (mt-10) REVERT: V 210 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9028 (tmmt) REVERT: W 30 ASN cc_start: 0.8802 (t0) cc_final: 0.8386 (t0) REVERT: W 105 VAL cc_start: 0.9154 (t) cc_final: 0.8913 (p) REVERT: W 123 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7885 (mp-120) REVERT: W 165 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8036 (mtm110) REVERT: W 181 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (mmtp) REVERT: W 205 ASP cc_start: 0.9150 (t0) cc_final: 0.8917 (t0) REVERT: X 33 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8703 (mtm110) REVERT: X 34 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8758 (tm-30) REVERT: X 130 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8435 (ttp-170) REVERT: X 181 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (mtpm) REVERT: X 184 GLN cc_start: 0.9169 (tt0) cc_final: 0.8840 (pm20) REVERT: Y 128 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8402 (mmp-170) REVERT: Y 129 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8489 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8365 (ttt180) REVERT: Y 147 ASP cc_start: 0.9174 (m-30) cc_final: 0.8588 (m-30) REVERT: Y 151 GLN cc_start: 0.9099 (mm110) cc_final: 0.8898 (tt0) REVERT: Y 165 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8155 (mtm110) REVERT: Y 181 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mmmt) REVERT: Y 184 GLN cc_start: 0.9202 (tt0) cc_final: 0.8904 (pm20) REVERT: Z 30 ASN cc_start: 0.8947 (t0) cc_final: 0.8514 (t0) REVERT: Z 109 GLU cc_start: 0.8653 (pt0) cc_final: 0.8355 (pm20) REVERT: Z 110 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7038 (mp) REVERT: Z 128 ARG cc_start: 0.8743 (tpt170) cc_final: 0.8513 (mmm160) REVERT: Z 151 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8879 (tt0) REVERT: Z 165 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7656 (mtm110) REVERT: Z 181 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mtpm) REVERT: Z 184 GLN cc_start: 0.9159 (tt0) cc_final: 0.8937 (pm20) REVERT: Z 210 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9079 (tmmt) outliers start: 80 outliers final: 12 residues processed: 405 average time/residue: 1.2953 time to fit residues: 557.0927 Evaluate side-chains 284 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 LYS Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 153 ASN Chi-restraints excluded: chain V residue 181 LYS Chi-restraints excluded: chain V residue 210 LYS Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 67 LYS Chi-restraints excluded: chain W residue 123 GLN Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain W residue 233 VAL Chi-restraints excluded: chain X residue 33 ARG Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 67 LYS Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 153 ASN Chi-restraints excluded: chain Z residue 181 LYS Chi-restraints excluded: chain Z residue 210 LYS Chi-restraints excluded: chain Z residue 233 VAL 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: 0.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 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: 0.7180 ------------------------------------------------------------------------------- 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 W 6 GLN W 247 HIS X 55 GLN X 247 HIS Y 247 HIS Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9920 Z= 0.233 Angle : 0.638 8.020 13425 Z= 0.335 Chirality : 0.044 0.200 1430 Planarity : 0.005 0.041 1705 Dihedral : 8.096 58.569 1369 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 5.51 % Allowed : 20.39 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1155 helix: 0.02 (0.21), residues: 535 sheet: 0.12 (0.27), residues: 320 loop : -0.87 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 156 HIS 0.005 0.001 HIS Z 247 PHE 0.017 0.002 PHE Y 195 TYR 0.023 0.002 TYR Y 157 ARG 0.006 0.001 ARG V 129 *********************** 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 394 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 337 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8839 (tm-30) REVERT: V 130 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8094 (ttt180) REVERT: V 147 ASP cc_start: 0.9002 (m-30) cc_final: 0.8660 (m-30) REVERT: V 151 GLN cc_start: 0.9072 (tt0) cc_final: 0.8842 (tt0) REVERT: V 196 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8731 (mt-10) REVERT: W 30 ASN cc_start: 0.8775 (t0) cc_final: 0.8513 (t0) REVERT: W 129 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8642 (ttp-110) REVERT: W 147 ASP cc_start: 0.8964 (m-30) cc_final: 0.8560 (m-30) REVERT: Y 129 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8502 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8318 (ttp-170) REVERT: Z 128 ARG cc_start: 0.8650 (tpt170) cc_final: 0.8426 (mmm160) REVERT: Z 129 ARG cc_start: 0.9193 (ttm-80) cc_final: 0.8811 (ttp-110) REVERT: Z 147 ASP cc_start: 0.8896 (m-30) cc_final: 0.8691 (m-30) REVERT: Z 165 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7601 (mtm110) REVERT: Z 196 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8756 (mt-10) outliers start: 57 outliers final: 19 residues processed: 373 average time/residue: 1.1323 time to fit residues: 452.2395 Evaluate side-chains 306 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 287 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 67 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 67 LYS Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 212 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 67 LYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 239 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 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 171 HIS V 247 HIS 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9920 Z= 0.308 Angle : 0.634 7.617 13425 Z= 0.324 Chirality : 0.044 0.284 1430 Planarity : 0.005 0.061 1705 Dihedral : 5.928 59.604 1318 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 6.09 % Allowed : 20.77 % Favored : 73.14 % 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: 0.57 (0.22), residues: 540 sheet: 0.06 (0.27), residues: 325 loop : -0.47 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 156 HIS 0.004 0.001 HIS Z 247 PHE 0.017 0.002 PHE V 225 TYR 0.020 0.002 TYR Y 157 ARG 0.008 0.001 ARG V 165 *********************** 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 358 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 295 time to evaluate : 1.111 Fit side-chains REVERT: V 34 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8863 (tm-30) REVERT: V 55 GLN cc_start: 0.9449 (mm-40) cc_final: 0.9032 (mp10) REVERT: V 130 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8031 (ttt180) REVERT: V 147 ASP cc_start: 0.9006 (m-30) cc_final: 0.8688 (m-30) REVERT: V 196 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8829 (mt-10) REVERT: W 30 ASN cc_start: 0.8769 (t0) cc_final: 0.8533 (t0) REVERT: W 129 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8662 (ttp-110) REVERT: W 207 LEU cc_start: 0.9000 (tp) cc_final: 0.8795 (tm) REVERT: W 210 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8817 (tptm) REVERT: Y 128 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8355 (mtt-85) REVERT: Y 129 ARG cc_start: 0.9072 (ttp-110) cc_final: 0.8658 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8291 (ttp-170) REVERT: Y 147 ASP cc_start: 0.8870 (m-30) cc_final: 0.8454 (m-30) REVERT: Z 129 ARG cc_start: 0.9223 (ttm-80) cc_final: 0.8858 (ttp-110) REVERT: Z 165 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7601 (mtm110) outliers start: 63 outliers final: 29 residues processed: 329 average time/residue: 1.1613 time to fit residues: 408.8420 Evaluate side-chains 307 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 212 LEU Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 239 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 55 GLN Z 241 ASN Z 247 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3959 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= 0.225 Angle : 0.590 7.419 13425 Z= 0.297 Chirality : 0.043 0.218 1430 Planarity : 0.005 0.050 1705 Dihedral : 4.564 20.304 1300 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 5.41 % Allowed : 22.42 % Favored : 72.17 % 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: 0.26 (0.24), residues: 1155 helix: 0.73 (0.22), residues: 535 sheet: -0.08 (0.26), residues: 325 loop : -0.24 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 156 HIS 0.005 0.001 HIS Z 247 PHE 0.016 0.001 PHE W 232 TYR 0.015 0.001 TYR Z 157 ARG 0.009 0.001 ARG W 165 *********************** 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 358 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 302 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8880 (tm-30) REVERT: V 110 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7377 (mp) REVERT: V 130 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7880 (ttt180) REVERT: W 30 ASN cc_start: 0.8742 (t0) cc_final: 0.8498 (t0) REVERT: W 129 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8679 (ttp-110) REVERT: W 176 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8098 (ptp90) REVERT: W 207 LEU cc_start: 0.8928 (tp) cc_final: 0.8718 (tm) REVERT: W 210 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8778 (tptm) REVERT: X 132 TYR cc_start: 0.8742 (m-80) cc_final: 0.8394 (m-80) REVERT: Y 128 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8339 (mtt-85) REVERT: Y 129 ARG cc_start: 0.9007 (ttp-110) cc_final: 0.8603 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8305 (ttp-170) REVERT: Y 174 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7187 (p) REVERT: Z 129 ARG cc_start: 0.9246 (ttm-80) cc_final: 0.8865 (ttp-110) REVERT: Z 161 MET cc_start: 0.7488 (mpt) cc_final: 0.7180 (mpt) REVERT: Z 165 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7436 (mtt-85) outliers start: 56 outliers final: 33 residues processed: 334 average time/residue: 1.1153 time to fit residues: 399.6217 Evaluate side-chains 322 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 67 LYS Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 211 LYS Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 212 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 207 LEU Chi-restraints excluded: chain Z residue 212 LEU 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: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 241 ASN V 247 HIS W 83 HIS X 241 ASN ** Z 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8783 moved from start: 0.3913 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= 0.356 Angle : 0.638 8.080 13425 Z= 0.323 Chirality : 0.043 0.205 1430 Planarity : 0.005 0.045 1705 Dihedral : 4.627 19.802 1300 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Rotamer: Outliers : 5.41 % Allowed : 23.67 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1155 helix: 0.68 (0.22), residues: 540 sheet: -0.12 (0.27), residues: 305 loop : 0.12 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 197 HIS 0.005 0.001 HIS Z 247 PHE 0.017 0.002 PHE V 143 TYR 0.017 0.002 TYR W 104 ARG 0.009 0.001 ARG W 165 *********************** 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 321 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8820 (tm-30) REVERT: V 130 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7925 (ttt180) REVERT: W 30 ASN cc_start: 0.8742 (t0) cc_final: 0.8535 (t0) REVERT: W 129 ARG cc_start: 0.9187 (ttm-80) cc_final: 0.8706 (ttp-110) REVERT: Y 128 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8403 (mtt-85) REVERT: Y 129 ARG cc_start: 0.9094 (ttp-110) cc_final: 0.8743 (ttm-80) REVERT: Y 174 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7206 (p) REVERT: Z 30 ASN cc_start: 0.8908 (t0) cc_final: 0.8572 (t0) REVERT: Z 129 ARG cc_start: 0.9287 (ttm-80) cc_final: 0.8902 (ttp-110) REVERT: Z 161 MET cc_start: 0.7558 (mpt) cc_final: 0.7301 (mpt) REVERT: Z 165 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7608 (mtm110) outliers start: 56 outliers final: 34 residues processed: 300 average time/residue: 1.1817 time to fit residues: 379.6642 Evaluate side-chains 290 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** Z 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8757 moved from start: 0.4107 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= 0.260 Angle : 0.619 10.326 13425 Z= 0.309 Chirality : 0.043 0.197 1430 Planarity : 0.005 0.046 1705 Dihedral : 4.530 19.701 1300 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 4.93 % Allowed : 24.35 % Favored : 70.72 % 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: 0.31 (0.24), residues: 1155 helix: 0.70 (0.22), residues: 540 sheet: -0.28 (0.26), residues: 305 loop : 0.22 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 197 HIS 0.005 0.001 HIS Z 247 PHE 0.014 0.002 PHE Z 225 TYR 0.017 0.002 TYR V 157 ARG 0.010 0.001 ARG W 165 *********************** 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: 51 poor density : 284 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8842 (tm-30) REVERT: V 110 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7500 (mp) REVERT: V 130 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7968 (ttt180) REVERT: W 30 ASN cc_start: 0.8743 (t0) cc_final: 0.8522 (t0) REVERT: W 129 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8707 (ttp-110) REVERT: W 176 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8006 (ptp90) REVERT: W 210 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8851 (tptp) REVERT: Y 128 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (mtt-85) REVERT: Y 129 ARG cc_start: 0.9097 (ttp-110) cc_final: 0.8746 (ttm-80) REVERT: Y 165 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7636 (mtm-85) REVERT: Y 174 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7201 (p) REVERT: Z 129 ARG cc_start: 0.9291 (ttm-80) cc_final: 0.8910 (ttp-110) REVERT: Z 161 MET cc_start: 0.7510 (mpt) cc_final: 0.7264 (mpt) REVERT: Z 165 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7651 (mtm110) REVERT: Z 220 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (tm-30) outliers start: 51 outliers final: 34 residues processed: 319 average time/residue: 1.1430 time to fit residues: 390.9067 Evaluate side-chains 316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain X residue 211 LYS Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 15 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: 0.8741 moved from start: 0.4227 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= 0.233 Angle : 0.632 10.376 13425 Z= 0.311 Chirality : 0.043 0.193 1430 Planarity : 0.005 0.048 1705 Dihedral : 4.478 19.564 1300 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 5.70 % Allowed : 25.80 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1155 helix: 0.68 (0.22), residues: 540 sheet: -0.33 (0.25), residues: 305 loop : 0.27 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 197 HIS 0.005 0.001 HIS Z 247 PHE 0.013 0.001 PHE Z 225 TYR 0.018 0.002 TYR V 144 ARG 0.011 0.001 ARG W 165 *********************** 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 341 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8819 (tm-30) REVERT: V 110 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7488 (mp) REVERT: V 130 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7986 (ttt180) REVERT: W 30 ASN cc_start: 0.8768 (t0) cc_final: 0.8563 (t0) REVERT: W 129 ARG cc_start: 0.9179 (ttm-80) cc_final: 0.8713 (ttp-110) REVERT: W 130 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7655 (ttt180) REVERT: W 176 ARG cc_start: 0.8530 (mtp85) cc_final: 0.7944 (ptp90) REVERT: W 210 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8850 (tptp) REVERT: Y 129 ARG cc_start: 0.9093 (ttp-110) cc_final: 0.8733 (ttm-80) REVERT: Y 165 ARG cc_start: 0.8142 (ttm170) cc_final: 0.7682 (mtm-85) REVERT: Y 174 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7128 (p) REVERT: Z 30 ASN cc_start: 0.8918 (t0) cc_final: 0.8591 (t0) REVERT: Z 129 ARG cc_start: 0.9291 (ttm-80) cc_final: 0.8913 (ttp-110) REVERT: Z 161 MET cc_start: 0.7470 (mpt) cc_final: 0.7122 (mpt) REVERT: Z 165 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7473 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8233 (ptp90) REVERT: Z 220 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (tm-30) outliers start: 59 outliers final: 40 residues processed: 325 average time/residue: 1.1436 time to fit residues: 398.1394 Evaluate side-chains 316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 184 GLN Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 220 GLU Chi-restraints excluded: chain Z residue 221 VAL 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: 0.0040 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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: 0.8736 moved from start: 0.4297 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= 0.237 Angle : 0.644 9.731 13425 Z= 0.318 Chirality : 0.043 0.203 1430 Planarity : 0.005 0.052 1705 Dihedral : 4.488 19.454 1300 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 5.31 % Allowed : 27.05 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1155 helix: 0.70 (0.22), residues: 540 sheet: -0.36 (0.25), residues: 305 loop : 0.32 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 197 HIS 0.006 0.001 HIS Z 247 PHE 0.016 0.002 PHE Z 195 TYR 0.012 0.002 TYR W 144 ARG 0.013 0.001 ARG W 165 *********************** 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 335 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 280 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8816 (tm-30) REVERT: V 110 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7468 (mp) REVERT: V 130 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7952 (ttt180) REVERT: W 129 ARG cc_start: 0.9173 (ttm-80) cc_final: 0.8712 (ttp-110) REVERT: W 176 ARG cc_start: 0.8516 (mtp85) cc_final: 0.7939 (ptp90) REVERT: W 210 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8855 (tptp) REVERT: Y 129 ARG cc_start: 0.9082 (ttp-110) cc_final: 0.8702 (ttm-80) REVERT: Y 158 MET cc_start: 0.7769 (mmm) cc_final: 0.7410 (mmm) REVERT: Y 165 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7766 (mtm110) REVERT: Y 174 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7130 (p) REVERT: Z 129 ARG cc_start: 0.9291 (ttm-80) cc_final: 0.8945 (ttp-110) REVERT: Z 161 MET cc_start: 0.7459 (mpt) cc_final: 0.7115 (mpt) REVERT: Z 165 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7496 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8757 (mtp85) cc_final: 0.8219 (ptp90) outliers start: 55 outliers final: 39 residues processed: 318 average time/residue: 1.1256 time to fit residues: 383.7852 Evaluate side-chains 314 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 83 HIS X 241 ASN Z 30 ASN Z 55 GLN Z 247 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 9920 Z= 0.518 Angle : 0.754 10.279 13425 Z= 0.378 Chirality : 0.047 0.241 1430 Planarity : 0.005 0.049 1705 Dihedral : 4.827 19.773 1300 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Rotamer: Outliers : 5.41 % Allowed : 27.73 % Favored : 66.86 % 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: 0.05 (0.23), residues: 1155 helix: 0.54 (0.22), residues: 545 sheet: -0.54 (0.25), residues: 305 loop : 0.15 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 197 HIS 0.006 0.001 HIS Z 247 PHE 0.022 0.002 PHE Z 195 TYR 0.021 0.002 TYR W 104 ARG 0.012 0.001 ARG V 165 *********************** 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 307 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 1.192 Fit side-chains REVERT: V 34 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8804 (tm-30) REVERT: V 55 GLN cc_start: 0.9412 (mm-40) cc_final: 0.8981 (mp10) REVERT: V 129 ARG cc_start: 0.9234 (ttm-80) cc_final: 0.8775 (tpm-80) REVERT: V 130 ARG cc_start: 0.8355 (mtp180) cc_final: 0.8070 (ttt180) REVERT: W 129 ARG cc_start: 0.9214 (ttm-80) cc_final: 0.8726 (ttp-110) REVERT: W 210 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8868 (tptp) REVERT: Y 129 ARG cc_start: 0.9154 (ttp-110) cc_final: 0.8718 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8392 (mtp180) REVERT: Y 174 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7200 (p) REVERT: Z 30 ASN cc_start: 0.8968 (t0) cc_final: 0.8640 (t0) REVERT: Z 129 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.8954 (ttp-110) REVERT: Z 161 MET cc_start: 0.7568 (mpt) cc_final: 0.7334 (mpt) REVERT: Z 165 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7640 (mtm110) REVERT: Z 176 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8186 (ptp90) outliers start: 56 outliers final: 42 residues processed: 292 average time/residue: 1.1659 time to fit residues: 364.5974 Evaluate side-chains 290 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 80 ASP Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 160 SER Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 192 LEU Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4402 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= 0.213 Angle : 0.669 10.037 13425 Z= 0.330 Chirality : 0.044 0.179 1430 Planarity : 0.005 0.057 1705 Dihedral : 4.623 19.791 1300 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.83 % Rotamer: Outliers : 4.06 % Allowed : 28.50 % Favored : 67.44 % 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: 0.21 (0.23), residues: 1155 helix: 0.66 (0.22), residues: 545 sheet: -0.40 (0.25), residues: 300 loop : 0.13 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP W 197 HIS 0.006 0.001 HIS Z 247 PHE 0.019 0.002 PHE Z 195 TYR 0.015 0.001 TYR Z 157 ARG 0.013 0.001 ARG W 165 ********************** 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 321 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 279 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: V 34 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8786 (tm-30) REVERT: V 130 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8044 (ttt180) REVERT: W 129 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8710 (ttp-110) REVERT: W 158 MET cc_start: 0.7990 (mmm) cc_final: 0.7718 (mmm) REVERT: W 176 ARG cc_start: 0.8514 (mtp85) cc_final: 0.7940 (ptp90) REVERT: X 129 ARG cc_start: 0.9003 (ttm-80) cc_final: 0.8425 (mmm-85) REVERT: X 176 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8067 (ptp90) REVERT: Y 129 ARG cc_start: 0.9093 (ttp-110) cc_final: 0.8639 (ttm-80) REVERT: Y 130 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8334 (mtp180) REVERT: Y 158 MET cc_start: 0.7700 (mmm) cc_final: 0.7301 (mmm) REVERT: Y 165 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7708 (mtm-85) REVERT: Y 174 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7130 (p) REVERT: Z 129 ARG cc_start: 0.9315 (ttm-80) cc_final: 0.8957 (ttp-110) REVERT: Z 147 ASP cc_start: 0.8803 (m-30) cc_final: 0.8561 (m-30) REVERT: Z 161 MET cc_start: 0.7432 (mpt) cc_final: 0.7088 (mpt) REVERT: Z 165 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7435 (mtt-85) REVERT: Z 176 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8198 (ptp90) outliers start: 42 outliers final: 30 residues processed: 309 average time/residue: 1.1480 time to fit residues: 380.0249 Evaluate side-chains 302 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 271 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain V residue 221 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 235 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 201 LEU Chi-restraints excluded: chain X residue 221 VAL Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ILE Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 221 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 184 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095606 restraints weight = 20360.538| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.28 r_work: 0.3393 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4481 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= 0.229 Angle : 0.672 9.811 13425 Z= 0.333 Chirality : 0.044 0.181 1430 Planarity : 0.005 0.056 1705 Dihedral : 4.591 22.679 1300 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Rotamer: Outliers : 4.06 % Allowed : 29.66 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1155 helix: 0.68 (0.22), residues: 545 sheet: -0.51 (0.25), residues: 310 loop : 0.39 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP W 197 HIS 0.007 0.001 HIS Z 247 PHE 0.018 0.002 PHE Z 195 TYR 0.015 0.001 TYR W 144 ARG 0.013 0.001 ARG W 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.11 seconds wall clock time: 101 minutes 2.48 seconds (6062.48 seconds total)