Starting phenix.real_space_refine on Thu Aug 6 12:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742.map" model { file = "/net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pms_71742/08_2026/9pms_71742_trim.cif" } resolution = 3.56 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 4666 2.51 5 N 1264 2.21 5 O 1507 1.98 5 H 7232 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14699 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3334 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 203} Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3263 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1777 Classifications: {'peptide': 113} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "H" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3182 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3101 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 206} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.35, per 1000 atoms: 0.16 Number of scatterers: 14699 At special positions: 0 Unit cell: (65.076, 90.882, 169.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1507 8.00 N 1264 7.00 C 4666 6.00 H 7232 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 202 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 85 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG C 201 " - " ASN C 60 " " NAG C 202 " - " ASN C 100 " " NAG C 203 " - " ASN C 23 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 363.5 milliseconds 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 22 sheets defined 9.5% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.229A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.700A pdb=" N LYS A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.801A pdb=" N GLN A 138 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.836A pdb=" N LEU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.777A pdb=" N GLU C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.582A pdb=" N LEU C 108 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.778A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.245A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.890A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.553A pdb=" N THR A 117 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 34 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.553A pdb=" N THR A 117 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 109 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 5.878A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLN B 27 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N SER B 67 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N ILE B 29 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N GLY B 65 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.599A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 4.019A pdb=" N ASN B 137 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 132 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER B 174 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.354A pdb=" N TRP B 148 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.829A pdb=" N SER C 5 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 11 Processing sheet with id=AB4, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.860A pdb=" N PHE C 33 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 46 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 31 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.527A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.607A pdb=" N ILE H 34 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.339A pdb=" N THR H 142 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL H 188 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY H 144 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL H 186 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 150 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU H 175 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR H 181 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA H 173 " --> pdb=" O THR H 181 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER H 183 " --> pdb=" O PHE H 171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.891A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 14 removed outlier: 5.946A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA L 50 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.173A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154 286 hydrogen bonds defined for protein. 699 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: 2.70 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 1784 1.05 - 1.24: 6510 1.24 - 1.44: 2257 1.44 - 1.63: 4276 1.63 - 1.82: 40 Bond restraints: 14867 Sorted by residual: bond pdb=" N GLY A 134 " pdb=" H GLY A 134 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR H 58 " pdb=" H THR H 58 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG L 61 " pdb="HH12 ARG L 61 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU C 108 " pdb=" H LEU C 108 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL A 176 " pdb=" H VAL A 176 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 14862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 21387 2.34 - 4.68: 4238 4.68 - 7.02: 1006 7.02 - 9.36: 136 9.36 - 11.70: 3 Bond angle restraints: 26770 Sorted by residual: angle pdb=" N ILE H 34 " pdb=" CA ILE H 34 " pdb=" C ILE H 34 " ideal model delta sigma weight residual 109.78 121.48 -11.70 1.58e+00 4.01e-01 5.49e+01 angle pdb=" C TRP H 33 " pdb=" N ILE H 34 " pdb=" CA ILE H 34 " ideal model delta sigma weight residual 120.35 129.65 -9.30 1.39e+00 5.18e-01 4.48e+01 angle pdb=" CA ASP C 106 " pdb=" CB ASP C 106 " pdb=" CG ASP C 106 " ideal model delta sigma weight residual 112.60 118.86 -6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" CA ASN C 60 " pdb=" CB ASN C 60 " pdb=" CG ASN C 60 " ideal model delta sigma weight residual 112.60 118.68 -6.08 1.00e+00 1.00e+00 3.69e+01 angle pdb=" C PRO H 152 " pdb=" N GLU H 153 " pdb=" CA GLU H 153 " ideal model delta sigma weight residual 120.58 128.03 -7.45 1.32e+00 5.74e-01 3.18e+01 ... (remaining 26765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6597 17.89 - 35.78: 401 35.78 - 53.67: 120 53.67 - 71.56: 87 71.56 - 89.45: 9 Dihedral angle restraints: 7214 sinusoidal: 3883 harmonic: 3331 Sorted by residual: dihedral pdb=" C ASP H 178 " pdb=" N ASP H 178 " pdb=" CA ASP H 178 " pdb=" CB ASP H 178 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA ALA H 107 " pdb=" C ALA H 107 " pdb=" N TRP H 108 " pdb=" CA TRP H 108 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR L 49 " pdb=" C TYR L 49 " pdb=" N ALA L 50 " pdb=" CA ALA L 50 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 887 0.109 - 0.217: 272 0.217 - 0.326: 39 0.326 - 0.435: 4 0.435 - 0.543: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA ASP H 178 " pdb=" N ASP H 178 " pdb=" C ASP H 178 " pdb=" CB ASP H 178 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA TYR L 49 " pdb=" N TYR L 49 " pdb=" C TYR L 49 " pdb=" CB TYR L 49 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA ASP A 180 " pdb=" N ASP A 180 " pdb=" C ASP A 180 " pdb=" CB ASP A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1201 not shown) Planarity restraints: 2253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 103 " 0.471 9.50e-02 1.11e+02 3.96e-01 3.00e+03 pdb=" NE ARG B 103 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 103 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 103 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 103 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 103 " 0.751 2.00e-02 2.50e+03 pdb="HH12 ARG B 103 " -0.785 2.00e-02 2.50e+03 pdb="HH21 ARG B 103 " 0.079 2.00e-02 2.50e+03 pdb="HH22 ARG B 103 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 103 " 0.786 9.50e-02 1.11e+02 3.11e-01 6.93e+02 pdb=" NE ARG L 103 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG L 103 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG L 103 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG L 103 " -0.030 2.00e-02 2.50e+03 pdb="HH11 ARG L 103 " 0.299 2.00e-02 2.50e+03 pdb="HH12 ARG L 103 " -0.213 2.00e-02 2.50e+03 pdb="HH21 ARG L 103 " 0.191 2.00e-02 2.50e+03 pdb="HH22 ARG L 103 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 60 " -0.191 2.00e-02 2.50e+03 1.44e-01 3.12e+02 pdb=" CG ASN C 60 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 60 " 0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN C 60 " 0.121 2.00e-02 2.50e+03 pdb="HD21 ASN C 60 " 0.133 2.00e-02 2.50e+03 pdb=" C1 NAG C 201 " -0.211 2.00e-02 2.50e+03 ... (remaining 2250 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 895 2.18 - 2.79: 24755 2.79 - 3.39: 39153 3.39 - 4.00: 52491 4.00 - 4.60: 77284 Nonbonded interactions: 194578 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" HG SER H 76 " model vdw 1.575 2.450 nonbonded pdb=" OD2 ASP A 73 " pdb=" HG SER A 76 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP L 110 " pdb=" HG1 THR L 200 " model vdw 1.592 2.450 nonbonded pdb=" HG SER L 121 " pdb=" OE1 GLU L 123 " model vdw 1.596 2.450 nonbonded pdb=" HG SER B 121 " pdb=" OE1 GLU B 123 " model vdw 1.605 2.450 ... (remaining 194573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 25 or resid 33 through 51 or resid 58 through 98 \ or resid 106 or resid 110 through 220)) selection = (chain 'H' and (resid 1 through 25 or resid 33 through 51 or resid 58 through 98 \ or resid 106 or resid 108 through 218)) } ncs_group { reference = (chain 'B' and (resid 1 through 23 or resid 25 or resid 35 through 49 or resid 5 \ 7 through 88 or resid 98 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 190 through 197 or (resid 198 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2) \ ) or resid 199 through 214)) selection = (chain 'L' and (resid 1 through 23 or resid 25 or resid 35 through 49 or resid 5 \ 7 through 88 or resid 98 through 214)) } 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 group one per residue 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: 4.840 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.012 0.069 7648 Z= 0.762 Angle : 1.930 11.702 10436 Z= 1.274 Chirality : 0.100 0.543 1204 Planarity : 0.016 0.330 1326 Dihedral : 12.895 87.798 2760 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.81 % Rotamer: Outliers : 0.60 % Allowed : 4.59 % Favored : 94.81 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.27), residues: 969 helix: -2.58 (0.65), residues: 27 sheet: 0.49 (0.26), residues: 396 loop : -0.94 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.145 0.019 TYR C 31 PHE 0.065 0.012 PHE C 61 TRP 0.111 0.020 TRP A 47 HIS 0.014 0.004 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.01240 / 0.76 ( 7635) covalent geometry : angle 1.92472 / 1.27 (10407) SS BOND : bond 0.01150 / 0.63 ( 10) SS BOND : angle 1.58953 / 1.02 ( 20) hydrogen bonds : bond 0.15684 / 10.30 ( 266) hydrogen bonds : angle 8.51665 / 5.90 ( 699) link_NAG-ASN : bond 0.01362 / 0.66 ( 3) link_NAG-ASN : angle 5.39464 / 3.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8797 (mtm) cc_final: 0.8589 (mtm) REVERT: B 140 TYR cc_start: 0.8325 (t80) cc_final: 0.7953 (t80) REVERT: B 209 PHE cc_start: 0.7168 (p90) cc_final: 0.6769 (p90) REVERT: H 13 ARG cc_start: 0.7449 (tpp-160) cc_final: 0.7244 (tpp-160) REVERT: H 34 ILE cc_start: 0.8553 (tt) cc_final: 0.8319 (tt) REVERT: H 60 TYR cc_start: 0.8475 (m-80) cc_final: 0.7168 (m-80) REVERT: H 138 ASN cc_start: 0.6990 (m110) cc_final: 0.6603 (m-40) REVERT: H 151 PHE cc_start: 0.8727 (t80) cc_final: 0.8226 (t80) REVERT: L 4 MET cc_start: 0.7854 (mmm) cc_final: 0.7633 (mmm) REVERT: L 147 LYS cc_start: 0.6466 (ttmm) cc_final: 0.6206 (ttmm) outliers start: 5 outliers final: 4 residues processed: 151 average time/residue: 0.1900 time to fit residues: 37.7124 Evaluate side-chains 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN H 43 GLN L 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128102 restraints weight = 30257.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133349 restraints weight = 15086.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136526 restraints weight = 9659.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138349 restraints weight = 7282.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139265 restraints weight = 6154.628| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 7648 Z= 0.191 Angle : 0.750 9.773 10436 Z= 0.410 Chirality : 0.046 0.196 1204 Planarity : 0.006 0.107 1326 Dihedral : 8.242 59.178 1123 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 1.09 % Allowed : 7.85 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 969 helix: -1.84 (0.77), residues: 33 sheet: 0.06 (0.24), residues: 463 loop : -1.21 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 103 TYR 0.027 0.002 TYR L 49 PHE 0.011 0.001 PHE C 61 TRP 0.017 0.002 TRP A 33 HIS 0.011 0.002 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 7635) covalent geometry : angle 0.73973 / 0.41 (10407) SS BOND : bond 0.00729 / 0.46 ( 10) SS BOND : angle 1.22410 / 0.84 ( 20) hydrogen bonds : bond 0.04716 / 3.10 ( 266) hydrogen bonds : angle 7.03820 / 4.81 ( 699) link_NAG-ASN : bond 0.00241 / 0.11 ( 3) link_NAG-ASN : angle 3.96927 / 2.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8443 (m-80) cc_final: 0.8033 (m-80) REVERT: H 138 ASN cc_start: 0.6894 (m110) cc_final: 0.6493 (m-40) REVERT: L 3 GLN cc_start: 0.7503 (mt0) cc_final: 0.7241 (mt0) outliers start: 9 outliers final: 8 residues processed: 117 average time/residue: 0.1698 time to fit residues: 26.7551 Evaluate side-chains 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128488 restraints weight = 29657.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133291 restraints weight = 14874.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136264 restraints weight = 9569.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137794 restraints weight = 7238.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138892 restraints weight = 6152.425| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7648 Z= 0.151 Angle : 0.634 7.489 10436 Z= 0.340 Chirality : 0.045 0.178 1204 Planarity : 0.005 0.037 1326 Dihedral : 7.435 58.309 1120 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.45 % Allowed : 8.57 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 969 helix: -1.24 (0.91), residues: 33 sheet: -0.04 (0.24), residues: 462 loop : -1.05 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 61 TYR 0.025 0.002 TYR B 140 PHE 0.010 0.001 PHE L 135 TRP 0.011 0.001 TRP H 33 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7635) covalent geometry : angle 0.62703 / 0.34 (10407) SS BOND : bond 0.00615 / 0.42 ( 10) SS BOND : angle 0.99641 / 0.71 ( 20) hydrogen bonds : bond 0.03768 / 2.44 ( 266) hydrogen bonds : angle 6.36412 / 4.34 ( 699) link_NAG-ASN : bond 0.00323 / 0.15 ( 3) link_NAG-ASN : angle 3.10166 / 1.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7627 (tpp) cc_final: 0.7353 (mmt) REVERT: H 13 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7258 (tpp-160) REVERT: H 60 TYR cc_start: 0.8440 (m-80) cc_final: 0.8027 (m-80) REVERT: H 81 MET cc_start: 0.7386 (ttp) cc_final: 0.7145 (ttp) REVERT: H 138 ASN cc_start: 0.6864 (m110) cc_final: 0.6464 (m-40) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.1670 time to fit residues: 25.8268 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128450 restraints weight = 30364.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133598 restraints weight = 15310.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136680 restraints weight = 9792.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138609 restraints weight = 7383.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139422 restraints weight = 6171.863| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7648 Z= 0.150 Angle : 0.592 6.875 10436 Z= 0.316 Chirality : 0.044 0.163 1204 Planarity : 0.004 0.037 1326 Dihedral : 6.915 58.340 1120 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.45 % Allowed : 9.42 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 969 helix: -1.26 (0.91), residues: 34 sheet: -0.04 (0.24), residues: 459 loop : -0.92 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.022 0.001 TYR L 49 PHE 0.008 0.001 PHE C 45 TRP 0.010 0.001 TRP L 148 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7635) covalent geometry : angle 0.58394 / 0.31 (10407) SS BOND : bond 0.00708 / 0.53 ( 10) SS BOND : angle 1.24204 / 0.73 ( 20) hydrogen bonds : bond 0.03419 / 2.19 ( 266) hydrogen bonds : angle 5.99702 / 4.08 ( 699) link_NAG-ASN : bond 0.00258 / 0.12 ( 3) link_NAG-ASN : angle 3.00230 / 1.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8435 (m-80) cc_final: 0.8032 (m-80) REVERT: H 138 ASN cc_start: 0.6703 (m110) cc_final: 0.6249 (m-40) outliers start: 12 outliers final: 11 residues processed: 116 average time/residue: 0.1797 time to fit residues: 27.3649 Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124892 restraints weight = 29583.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129636 restraints weight = 14995.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132479 restraints weight = 9681.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134116 restraints weight = 7341.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134951 restraints weight = 6220.225| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7648 Z= 0.202 Angle : 0.612 6.729 10436 Z= 0.327 Chirality : 0.045 0.142 1204 Planarity : 0.005 0.041 1326 Dihedral : 6.796 58.213 1120 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.57 % Allowed : 10.99 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 969 helix: -1.24 (0.88), residues: 34 sheet: -0.07 (0.24), residues: 458 loop : -0.94 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 211 TYR 0.029 0.002 TYR L 49 PHE 0.009 0.001 PHE L 135 TRP 0.011 0.002 TRP A 33 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 7635) covalent geometry : angle 0.60444 / 0.33 (10407) SS BOND : bond 0.00570 / 0.38 ( 10) SS BOND : angle 1.23570 / 0.73 ( 20) hydrogen bonds : bond 0.03470 / 2.25 ( 266) hydrogen bonds : angle 5.96107 / 4.02 ( 699) link_NAG-ASN : bond 0.00129 / 0.06 ( 3) link_NAG-ASN : angle 2.99914 / 1.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7215 (t80) cc_final: 0.6914 (t80) REVERT: H 60 TYR cc_start: 0.8508 (m-80) cc_final: 0.7987 (m-80) REVERT: H 138 ASN cc_start: 0.6566 (m110) cc_final: 0.6125 (m-40) REVERT: L 186 TYR cc_start: 0.8086 (t80) cc_final: 0.7847 (t80) outliers start: 13 outliers final: 13 residues processed: 110 average time/residue: 0.1755 time to fit residues: 26.0309 Evaluate side-chains 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126639 restraints weight = 30416.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131749 restraints weight = 15303.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134845 restraints weight = 9860.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136698 restraints weight = 7445.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137528 restraints weight = 6258.080| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7648 Z= 0.158 Angle : 0.584 6.382 10436 Z= 0.309 Chirality : 0.044 0.143 1204 Planarity : 0.004 0.041 1326 Dihedral : 6.593 58.264 1120 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.21 % Allowed : 11.96 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.28), residues: 969 helix: -1.29 (0.88), residues: 34 sheet: 0.02 (0.24), residues: 460 loop : -0.86 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 40 TYR 0.024 0.002 TYR L 49 PHE 0.008 0.001 PHE C 45 TRP 0.010 0.001 TRP A 33 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7635) covalent geometry : angle 0.57613 / 0.31 (10407) SS BOND : bond 0.00468 / 0.28 ( 10) SS BOND : angle 1.00644 / 0.62 ( 20) hydrogen bonds : bond 0.03229 / 2.08 ( 266) hydrogen bonds : angle 5.83943 / 3.95 ( 699) link_NAG-ASN : bond 0.00175 / 0.08 ( 3) link_NAG-ASN : angle 2.96937 / 1.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7304 (t80) cc_final: 0.7005 (t80) REVERT: H 60 TYR cc_start: 0.8480 (m-80) cc_final: 0.7948 (m-80) REVERT: H 138 ASN cc_start: 0.6526 (m110) cc_final: 0.6062 (m-40) REVERT: L 148 TRP cc_start: 0.7207 (m100) cc_final: 0.6227 (m100) REVERT: L 186 TYR cc_start: 0.8110 (t80) cc_final: 0.7879 (t80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.1669 time to fit residues: 23.6899 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126288 restraints weight = 30353.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131301 restraints weight = 15262.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134324 restraints weight = 9814.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136128 restraints weight = 7428.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136975 restraints weight = 6249.949| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7648 Z= 0.166 Angle : 0.579 6.151 10436 Z= 0.307 Chirality : 0.044 0.143 1204 Planarity : 0.004 0.043 1326 Dihedral : 6.440 58.133 1120 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 1.33 % Allowed : 12.44 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 969 helix: -1.29 (0.89), residues: 34 sheet: 0.05 (0.25), residues: 441 loop : -0.79 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 211 TYR 0.026 0.002 TYR L 49 PHE 0.009 0.001 PHE C 45 TRP 0.011 0.001 TRP A 33 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 7635) covalent geometry : angle 0.57161 / 0.30 (10407) SS BOND : bond 0.00640 / 0.47 ( 10) SS BOND : angle 1.01009 / 0.62 ( 20) hydrogen bonds : bond 0.03173 / 2.05 ( 266) hydrogen bonds : angle 5.77001 / 3.89 ( 699) link_NAG-ASN : bond 0.00223 / 0.11 ( 3) link_NAG-ASN : angle 2.99722 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7374 (t80) cc_final: 0.7106 (t80) REVERT: H 60 TYR cc_start: 0.8483 (m-80) cc_final: 0.7929 (m-80) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.1825 time to fit residues: 26.0519 Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126104 restraints weight = 30416.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131121 restraints weight = 15348.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134185 restraints weight = 9863.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135753 restraints weight = 7458.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136752 restraints weight = 6352.503| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7648 Z= 0.174 Angle : 0.585 5.968 10436 Z= 0.310 Chirality : 0.044 0.144 1204 Planarity : 0.004 0.042 1326 Dihedral : 6.369 57.959 1120 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 1.57 % Allowed : 12.80 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 969 helix: -1.26 (0.86), residues: 34 sheet: 0.03 (0.25), residues: 441 loop : -0.82 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.027 0.002 TYR L 49 PHE 0.009 0.001 PHE C 45 TRP 0.011 0.001 TRP A 33 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 7635) covalent geometry : angle 0.57737 / 0.31 (10407) SS BOND : bond 0.00500 / 0.34 ( 10) SS BOND : angle 1.02872 / 0.64 ( 20) hydrogen bonds : bond 0.03187 / 2.07 ( 266) hydrogen bonds : angle 5.75163 / 3.88 ( 699) link_NAG-ASN : bond 0.00190 / 0.09 ( 3) link_NAG-ASN : angle 3.02000 / 1.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7409 (t80) cc_final: 0.7157 (t80) REVERT: H 60 TYR cc_start: 0.8493 (m-80) cc_final: 0.7938 (m-80) REVERT: L 211 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7102 (ttp80) outliers start: 13 outliers final: 13 residues processed: 108 average time/residue: 0.1816 time to fit residues: 26.2882 Evaluate side-chains 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125203 restraints weight = 29706.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129942 restraints weight = 15010.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132813 restraints weight = 9639.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134394 restraints weight = 7274.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135449 restraints weight = 6154.222| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7648 Z= 0.160 Angle : 0.585 6.020 10436 Z= 0.308 Chirality : 0.044 0.146 1204 Planarity : 0.004 0.045 1326 Dihedral : 6.265 57.883 1120 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.97 % Allowed : 13.53 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 969 helix: -1.19 (0.86), residues: 34 sheet: 0.03 (0.25), residues: 442 loop : -0.77 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 103 TYR 0.025 0.001 TYR L 49 PHE 0.009 0.001 PHE C 45 TRP 0.011 0.001 TRP A 33 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7635) covalent geometry : angle 0.57733 / 0.31 (10407) SS BOND : bond 0.00446 / 0.29 ( 10) SS BOND : angle 0.98229 / 0.62 ( 20) hydrogen bonds : bond 0.03097 / 2.01 ( 266) hydrogen bonds : angle 5.71566 / 3.85 ( 699) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 2.98057 / 1.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7340 (t80) cc_final: 0.7113 (t80) REVERT: H 60 TYR cc_start: 0.8486 (m-80) cc_final: 0.7919 (m-80) REVERT: L 211 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6995 (ttp80) outliers start: 8 outliers final: 8 residues processed: 103 average time/residue: 0.1720 time to fit residues: 23.8418 Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.0040 chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127893 restraints weight = 30331.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133007 restraints weight = 15190.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136106 restraints weight = 9721.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137903 restraints weight = 7309.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138828 restraints weight = 6159.638| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7648 Z= 0.122 Angle : 0.564 7.096 10436 Z= 0.294 Chirality : 0.044 0.148 1204 Planarity : 0.004 0.046 1326 Dihedral : 6.099 58.277 1120 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 1.09 % Allowed : 13.04 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.28), residues: 969 helix: -1.09 (0.88), residues: 34 sheet: 0.11 (0.25), residues: 441 loop : -0.67 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 40 TYR 0.018 0.001 TYR L 49 PHE 0.010 0.001 PHE C 45 TRP 0.010 0.001 TRP A 33 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 7635) covalent geometry : angle 0.55653 / 0.29 (10407) SS BOND : bond 0.00469 / 0.34 ( 10) SS BOND : angle 0.82114 / 0.53 ( 20) hydrogen bonds : bond 0.02897 / 1.88 ( 266) hydrogen bonds : angle 5.59493 / 3.79 ( 699) link_NAG-ASN : bond 0.00252 / 0.12 ( 3) link_NAG-ASN : angle 2.95792 / 1.77 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7379 (t80) cc_final: 0.7138 (t80) REVERT: H 60 TYR cc_start: 0.8449 (m-80) cc_final: 0.7858 (m-80) REVERT: L 211 ARG cc_start: 0.7356 (ttp80) cc_final: 0.7018 (ttp80) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.1743 time to fit residues: 24.5626 Evaluate side-chains 102 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 34 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128547 restraints weight = 30222.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133632 restraints weight = 15064.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136714 restraints weight = 9581.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138331 restraints weight = 7203.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139448 restraints weight = 6101.333| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7648 Z= 0.154 Angle : 0.583 6.378 10436 Z= 0.306 Chirality : 0.044 0.143 1204 Planarity : 0.004 0.046 1326 Dihedral : 5.906 57.719 1118 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 1.09 % Allowed : 13.53 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 969 helix: -1.14 (0.84), residues: 35 sheet: 0.09 (0.25), residues: 442 loop : -0.69 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.024 0.001 TYR L 49 PHE 0.010 0.001 PHE C 45 TRP 0.010 0.001 TRP A 33 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 7635) covalent geometry : angle 0.57557 / 0.30 (10407) SS BOND : bond 0.00473 / 0.33 ( 10) SS BOND : angle 0.96674 / 0.61 ( 20) hydrogen bonds : bond 0.02963 / 1.93 ( 266) hydrogen bonds : angle 5.60365 / 3.79 ( 699) link_NAG-ASN : bond 0.00202 / 0.10 ( 3) link_NAG-ASN : angle 2.97367 / 1.80 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.37 seconds wall clock time: 43 minutes 49.04 seconds (2629.04 seconds total)