Starting phenix.real_space_refine on Sat Mar 16 00:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/03_2024/6xzc_10658.pdb" } resolution = 3.37 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= 0.001 sd= 0.100 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 49 5.16 5 C 8302 2.51 5 N 2359 2.21 5 O 2569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ASP 228": "OD1" <-> "OD2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 138": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "G ASP 228": "OD1" <-> "OD2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 7.41, per 1000 atoms: 0.56 Number of scatterers: 13279 At special positions: 0 Unit cell: (111.09, 110.032, 112.148, 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 49 16.00 O 2569 8.00 N 2359 7.00 C 8302 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: 5.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 155 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 246 through 268 Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 160 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 246 through 268 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.635A pdb=" N ASP F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 155 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 160 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA F 183 " --> pdb=" O ASP F 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 246 through 268 Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 155 " --> pdb=" O HIS G 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN G 160 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 161 " --> pdb=" O ASN G 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 166 " --> pdb=" O THR G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 243 Processing helix chain 'G' and resid 246 through 268 952 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4566 1.34 - 1.46: 1663 1.46 - 1.57: 7267 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 13580 Sorted by residual: bond pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.38e+00 bond pdb=" CA GLU G 127 " pdb=" C GLU G 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.36e+00 bond pdb=" CA GLU D 127 " pdb=" C GLU D 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.29e+00 bond pdb=" CA GLU C 127 " pdb=" C GLU C 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.26e+00 bond pdb=" CA GLU E 127 " pdb=" C GLU E 127 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.10e-02 2.27e+03 2.22e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 658 107.00 - 113.76: 7326 113.76 - 120.52: 5959 120.52 - 127.28: 4355 127.28 - 134.04: 196 Bond angle restraints: 18494 Sorted by residual: angle pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 7.02e+00 angle pdb=" CA GLU G 127 " pdb=" C GLU G 127 " pdb=" N PRO G 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU D 127 " pdb=" C GLU D 127 " pdb=" N PRO D 128 " ideal model delta sigma weight residual 116.90 120.86 -3.96 1.50e+00 4.44e-01 6.96e+00 angle pdb=" CA GLU C 127 " pdb=" C GLU C 127 " pdb=" N PRO C 128 " ideal model delta sigma weight residual 116.90 120.83 -3.93 1.50e+00 4.44e-01 6.86e+00 ... (remaining 18489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 7559 13.87 - 27.74: 575 27.74 - 41.62: 203 41.62 - 55.49: 42 55.49 - 69.36: 28 Dihedral angle restraints: 8407 sinusoidal: 3409 harmonic: 4998 Sorted by residual: dihedral pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " pdb=" OD1 ASP A 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.83 57.83 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP G 228 " pdb=" CB ASP G 228 " pdb=" CG ASP G 228 " pdb=" OD1 ASP G 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " pdb=" OD1 ASP C 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 8404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1128 0.026 - 0.051: 558 0.051 - 0.077: 162 0.077 - 0.103: 99 0.103 - 0.129: 41 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CB ILE B 282 " pdb=" CA ILE B 282 " pdb=" CG1 ILE B 282 " pdb=" CG2 ILE B 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CB ILE C 282 " pdb=" CA ILE C 282 " pdb=" CG1 ILE C 282 " pdb=" CG2 ILE C 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CB ILE E 282 " pdb=" CA ILE E 282 " pdb=" CG1 ILE E 282 " pdb=" CG2 ILE E 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1985 not shown) Planarity restraints: 2513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 247 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO E 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 247 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO F 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 247 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 248 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.034 5.00e-02 4.00e+02 ... (remaining 2510 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4243 2.84 - 3.35: 12529 3.35 - 3.87: 21661 3.87 - 4.38: 23214 4.38 - 4.90: 40794 Nonbonded interactions: 102441 Sorted by model distance: nonbonded pdb=" OD1 ASN B 129 " pdb=" OH TYR B 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN E 129 " pdb=" OH TYR E 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN D 129 " pdb=" OH TYR D 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN A 129 " pdb=" OH TYR A 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN F 129 " pdb=" OH TYR F 250 " model vdw 2.323 2.440 ... (remaining 102436 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 3.380 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: 14.230 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.720 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.004 0.041 13580 Z= 0.280 Angle : 0.628 5.872 18494 Z= 0.372 Chirality : 0.038 0.129 1988 Planarity : 0.007 0.059 2513 Dihedral : 12.496 69.359 5145 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.06 % Allowed : 8.16 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 1666 helix: -1.20 (0.11), residues: 1176 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 156 HIS 0.006 0.002 HIS D 216 PHE 0.017 0.002 PHE A 152 TYR 0.009 0.001 TYR C 236 ARG 0.003 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 334 time to evaluate : 1.409 Fit side-chains REVERT: A 56 MET cc_start: 0.8450 (tpp) cc_final: 0.8180 (mmm) REVERT: A 59 TYR cc_start: 0.7568 (m-80) cc_final: 0.7312 (m-10) REVERT: B 239 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6026 (p0) REVERT: C 25 MET cc_start: 0.7045 (mtp) cc_final: 0.6653 (mtt) REVERT: C 239 ASN cc_start: 0.5388 (OUTLIER) cc_final: 0.5133 (p0) REVERT: D 56 MET cc_start: 0.7297 (tpp) cc_final: 0.6868 (tpt) REVERT: D 131 MET cc_start: 0.6279 (mmm) cc_final: 0.5790 (mpp) REVERT: D 236 TYR cc_start: 0.5940 (t80) cc_final: 0.5553 (t80) REVERT: D 286 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7625 (Cg_endo) REVERT: E 131 MET cc_start: 0.6574 (mmm) cc_final: 0.6243 (mpp) REVERT: E 286 PRO cc_start: 0.8418 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: F 131 MET cc_start: 0.6548 (mmm) cc_final: 0.6194 (mpp) REVERT: G 56 MET cc_start: 0.8239 (tpp) cc_final: 0.8027 (mmm) REVERT: G 255 GLN cc_start: 0.7426 (tt0) cc_final: 0.7223 (tm-30) outliers start: 42 outliers final: 1 residues processed: 357 average time/residue: 0.2553 time to fit residues: 127.9518 Evaluate side-chains 179 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain G residue 84 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 216 HIS B 48 GLN B 216 HIS C 216 HIS C 274 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN E 48 GLN E 216 HIS F 48 GLN F 175 ASN F 216 HIS G 216 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13580 Z= 0.217 Angle : 0.549 6.504 18494 Z= 0.283 Chirality : 0.034 0.135 1988 Planarity : 0.005 0.064 2513 Dihedral : 3.657 22.661 1839 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.46 % Allowed : 12.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 1666 helix: 1.84 (0.13), residues: 1204 sheet: None (None), residues: 0 loop : -0.06 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.011 0.001 HIS B 151 PHE 0.022 0.002 PHE D 130 TYR 0.034 0.002 TYR A 226 ARG 0.006 0.001 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8352 (tpp) cc_final: 0.7961 (mmm) REVERT: A 59 TYR cc_start: 0.8157 (m-80) cc_final: 0.7683 (m-80) REVERT: A 254 GLN cc_start: 0.8121 (tp40) cc_final: 0.7775 (tp40) REVERT: B 239 ASN cc_start: 0.6509 (OUTLIER) cc_final: 0.6226 (p0) REVERT: D 131 MET cc_start: 0.6405 (mmm) cc_final: 0.5973 (mpp) REVERT: E 56 MET cc_start: 0.9022 (tpp) cc_final: 0.8778 (tpp) REVERT: E 131 MET cc_start: 0.6789 (mmm) cc_final: 0.6359 (mpp) REVERT: E 255 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7784 (tp40) REVERT: F 56 MET cc_start: 0.8991 (tpp) cc_final: 0.8553 (mmm) REVERT: F 131 MET cc_start: 0.6550 (mmm) cc_final: 0.6227 (mpp) REVERT: F 151 HIS cc_start: 0.8048 (t-90) cc_final: 0.7716 (t-90) REVERT: G 25 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: G 59 TYR cc_start: 0.8271 (m-80) cc_final: 0.8013 (m-80) REVERT: G 235 LEU cc_start: 0.7649 (tp) cc_final: 0.7387 (tt) REVERT: G 255 GLN cc_start: 0.7891 (tt0) cc_final: 0.7532 (tp40) outliers start: 20 outliers final: 7 residues processed: 203 average time/residue: 0.2274 time to fit residues: 69.2555 Evaluate side-chains 167 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 25 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 chunk 136 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 48 GLN B 151 HIS B 245 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN E 129 ASN E 245 GLN F 48 GLN F 175 ASN F 245 GLN G 245 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13580 Z= 0.347 Angle : 0.609 9.746 18494 Z= 0.308 Chirality : 0.038 0.159 1988 Planarity : 0.005 0.048 2513 Dihedral : 3.786 20.249 1836 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.84 % Allowed : 12.90 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.20), residues: 1666 helix: 2.49 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : 0.70 (0.33), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 156 HIS 0.014 0.002 HIS B 151 PHE 0.028 0.003 PHE D 152 TYR 0.028 0.002 TYR G 226 ARG 0.020 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.568 Fit side-chains REVERT: A 16 ASN cc_start: 0.8396 (m-40) cc_final: 0.8020 (m-40) REVERT: A 56 MET cc_start: 0.8739 (tpp) cc_final: 0.8240 (mmm) REVERT: A 198 MET cc_start: 0.8681 (mmm) cc_final: 0.7835 (mmt) REVERT: A 200 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8021 (ttmm) REVERT: A 234 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6969 (tpp80) REVERT: A 285 ASP cc_start: 0.7703 (m-30) cc_final: 0.7345 (p0) REVERT: B 239 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6514 (p0) REVERT: C 51 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 200 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: C 284 ILE cc_start: 0.8768 (mm) cc_final: 0.8530 (mt) REVERT: D 131 MET cc_start: 0.6530 (mmm) cc_final: 0.6189 (mpp) REVERT: E 131 MET cc_start: 0.6895 (mmm) cc_final: 0.6554 (mpp) REVERT: E 200 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7757 (mtpp) REVERT: E 255 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7592 (tp40) REVERT: F 73 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8801 (t) REVERT: F 200 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7701 (mttm) REVERT: F 254 GLN cc_start: 0.8103 (tp40) cc_final: 0.7656 (tp40) REVERT: G 198 MET cc_start: 0.8520 (mmt) cc_final: 0.8031 (mmt) REVERT: G 200 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: G 234 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.7149 (tpp80) REVERT: G 235 LEU cc_start: 0.7740 (tp) cc_final: 0.7485 (tt) REVERT: G 254 GLN cc_start: 0.8105 (tp40) cc_final: 0.7849 (tp-100) REVERT: G 255 GLN cc_start: 0.7948 (tt0) cc_final: 0.7574 (tp40) REVERT: G 285 ASP cc_start: 0.8110 (m-30) cc_final: 0.7734 (p0) outliers start: 39 outliers final: 18 residues processed: 203 average time/residue: 0.2585 time to fit residues: 75.5723 Evaluate side-chains 167 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 37 CYS Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 16 ASN B 48 GLN B 151 HIS C 48 GLN D 12 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13580 Z= 0.168 Angle : 0.468 7.472 18494 Z= 0.230 Chirality : 0.034 0.198 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.372 19.284 1836 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 1.02 % Allowed : 16.11 % Favored : 82.87 % 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: 4.11 (0.21), residues: 1666 helix: 3.36 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.06 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 156 HIS 0.006 0.001 HIS B 151 PHE 0.016 0.001 PHE C 152 TYR 0.013 0.001 TYR G 226 ARG 0.005 0.000 ARG F 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.367 Fit side-chains REVERT: A 16 ASN cc_start: 0.8342 (m-40) cc_final: 0.7979 (m-40) REVERT: A 198 MET cc_start: 0.8623 (mmm) cc_final: 0.7855 (mmt) REVERT: A 234 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.7001 (tpp80) REVERT: A 285 ASP cc_start: 0.7788 (m-30) cc_final: 0.7480 (p0) REVERT: B 284 ILE cc_start: 0.8834 (mm) cc_final: 0.8556 (mt) REVERT: D 131 MET cc_start: 0.6599 (mmm) cc_final: 0.6362 (mpp) REVERT: D 247 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7050 (tt) REVERT: E 131 MET cc_start: 0.6848 (mmm) cc_final: 0.6486 (mpp) REVERT: E 252 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8244 (tm-30) REVERT: E 254 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7243 (tt0) REVERT: F 198 MET cc_start: 0.8437 (mmt) cc_final: 0.7934 (mmt) REVERT: F 254 GLN cc_start: 0.8083 (tp40) cc_final: 0.7655 (tt0) REVERT: F 285 ASP cc_start: 0.8264 (m-30) cc_final: 0.7967 (p0) REVERT: G 25 MET cc_start: 0.9162 (mtp) cc_final: 0.8888 (mtt) REVERT: G 226 TYR cc_start: 0.8293 (t80) cc_final: 0.8015 (t80) REVERT: G 234 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.7175 (tpp80) REVERT: G 235 LEU cc_start: 0.7524 (tp) cc_final: 0.7267 (tt) REVERT: G 285 ASP cc_start: 0.8108 (m-30) cc_final: 0.7749 (p0) outliers start: 14 outliers final: 5 residues processed: 159 average time/residue: 0.2170 time to fit residues: 52.7439 Evaluate side-chains 139 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 0.0370 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN G 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13580 Z= 0.155 Angle : 0.456 7.060 18494 Z= 0.220 Chirality : 0.033 0.195 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.188 12.323 1834 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.75 % Allowed : 16.03 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.21), residues: 1666 helix: 3.72 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.26 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.004 0.001 HIS D 216 PHE 0.015 0.001 PHE C 152 TYR 0.014 0.001 TYR G 226 ARG 0.005 0.000 ARG F 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.451 Fit side-chains REVERT: A 198 MET cc_start: 0.8582 (mmm) cc_final: 0.7806 (mmt) REVERT: A 234 ARG cc_start: 0.7326 (mmm-85) cc_final: 0.6971 (tpp80) REVERT: A 285 ASP cc_start: 0.7829 (m-30) cc_final: 0.7510 (p0) REVERT: B 284 ILE cc_start: 0.8907 (mm) cc_final: 0.8652 (mt) REVERT: E 131 MET cc_start: 0.6849 (mmm) cc_final: 0.6514 (mpp) REVERT: E 252 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8255 (tm-30) REVERT: E 254 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7302 (tt0) REVERT: F 198 MET cc_start: 0.8402 (mmt) cc_final: 0.7948 (mmt) REVERT: F 254 GLN cc_start: 0.8072 (tp40) cc_final: 0.7673 (tt0) REVERT: F 285 ASP cc_start: 0.8222 (m-30) cc_final: 0.7947 (p0) REVERT: G 25 MET cc_start: 0.9135 (mtp) cc_final: 0.8865 (mtt) REVERT: G 234 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.7138 (tpp80) REVERT: G 235 LEU cc_start: 0.7606 (tp) cc_final: 0.7342 (tt) REVERT: G 285 ASP cc_start: 0.8079 (m-30) cc_final: 0.7724 (p0) outliers start: 24 outliers final: 12 residues processed: 160 average time/residue: 0.2230 time to fit residues: 53.4972 Evaluate side-chains 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain G residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13580 Z= 0.156 Angle : 0.460 8.207 18494 Z= 0.220 Chirality : 0.034 0.209 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.115 12.741 1834 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.24 % Allowed : 16.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.21), residues: 1666 helix: 3.86 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.37 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 156 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE C 152 TYR 0.012 0.001 TYR C 59 ARG 0.007 0.000 ARG G 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8570 (mmm) cc_final: 0.7812 (mmt) REVERT: A 234 ARG cc_start: 0.7361 (mmm-85) cc_final: 0.6978 (tpp80) REVERT: A 285 ASP cc_start: 0.7851 (m-30) cc_final: 0.7551 (p0) REVERT: B 284 ILE cc_start: 0.8936 (mm) cc_final: 0.8686 (mt) REVERT: E 131 MET cc_start: 0.6764 (mmm) cc_final: 0.6428 (mpp) REVERT: E 254 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7328 (tt0) REVERT: E 255 GLN cc_start: 0.7729 (tp40) cc_final: 0.7418 (tt0) REVERT: F 254 GLN cc_start: 0.8029 (tp40) cc_final: 0.7673 (tt0) REVERT: F 285 ASP cc_start: 0.8207 (m-30) cc_final: 0.7944 (p0) REVERT: G 25 MET cc_start: 0.9097 (mtp) cc_final: 0.8869 (mtt) REVERT: G 234 ARG cc_start: 0.7503 (mmm-85) cc_final: 0.7151 (tpp80) REVERT: G 235 LEU cc_start: 0.7639 (tp) cc_final: 0.7373 (tt) REVERT: G 285 ASP cc_start: 0.8147 (m-30) cc_final: 0.7797 (p0) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.2190 time to fit residues: 49.1907 Evaluate side-chains 146 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 74 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13580 Z= 0.157 Angle : 0.455 7.326 18494 Z= 0.219 Chirality : 0.034 0.196 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.089 11.958 1834 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.60 % Allowed : 16.47 % Favored : 81.92 % 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: 4.93 (0.21), residues: 1666 helix: 3.96 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.39 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 156 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE C 152 TYR 0.020 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.532 Fit side-chains REVERT: A 198 MET cc_start: 0.8598 (mmm) cc_final: 0.7808 (mmt) REVERT: A 234 ARG cc_start: 0.7358 (mmm-85) cc_final: 0.6978 (tpp80) REVERT: A 285 ASP cc_start: 0.7866 (m-30) cc_final: 0.7570 (p0) REVERT: B 284 ILE cc_start: 0.8956 (mm) cc_final: 0.8706 (mt) REVERT: D 252 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 131 MET cc_start: 0.6757 (mmm) cc_final: 0.6418 (mpp) REVERT: E 254 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7319 (tt0) REVERT: E 255 GLN cc_start: 0.7717 (tp40) cc_final: 0.7412 (tt0) REVERT: F 138 ARG cc_start: 0.8463 (tmm-80) cc_final: 0.8149 (tmm160) REVERT: F 235 LEU cc_start: 0.7524 (tp) cc_final: 0.7274 (tt) REVERT: F 254 GLN cc_start: 0.8026 (tp40) cc_final: 0.7695 (tt0) REVERT: F 285 ASP cc_start: 0.8173 (m-30) cc_final: 0.7929 (p0) REVERT: G 234 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7174 (tpp80) REVERT: G 235 LEU cc_start: 0.7626 (tp) cc_final: 0.7367 (tt) REVERT: G 254 GLN cc_start: 0.7715 (tp40) cc_final: 0.7027 (tt0) REVERT: G 285 ASP cc_start: 0.8147 (m-30) cc_final: 0.7804 (p0) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.2283 time to fit residues: 52.0706 Evaluate side-chains 150 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN B 274 ASN C 48 GLN C 245 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13580 Z= 0.235 Angle : 0.501 8.256 18494 Z= 0.241 Chirality : 0.036 0.229 1988 Planarity : 0.003 0.037 2513 Dihedral : 3.248 13.742 1834 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.17 % Allowed : 16.91 % Favored : 81.92 % 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: 4.75 (0.21), residues: 1666 helix: 3.82 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.34 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.006 0.001 HIS C 216 PHE 0.015 0.002 PHE E 152 TYR 0.017 0.001 TYR G 226 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.464 Fit side-chains REVERT: A 254 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7122 (tt0) REVERT: A 285 ASP cc_start: 0.7946 (m-30) cc_final: 0.7643 (p0) REVERT: B 284 ILE cc_start: 0.9031 (mm) cc_final: 0.8788 (mt) REVERT: C 243 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7310 (ttm170) REVERT: D 151 HIS cc_start: 0.8043 (t70) cc_final: 0.7414 (m170) REVERT: D 252 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7819 (tm-30) REVERT: E 131 MET cc_start: 0.6791 (mmm) cc_final: 0.6458 (mpp) REVERT: E 235 LEU cc_start: 0.7768 (tp) cc_final: 0.7463 (tt) REVERT: E 254 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7352 (tt0) REVERT: E 255 GLN cc_start: 0.7760 (tp40) cc_final: 0.7456 (tt0) REVERT: F 73 SER cc_start: 0.9053 (t) cc_final: 0.8831 (t) REVERT: F 198 MET cc_start: 0.8483 (mmt) cc_final: 0.7987 (mmt) REVERT: F 235 LEU cc_start: 0.7662 (tp) cc_final: 0.7332 (tt) REVERT: F 254 GLN cc_start: 0.8033 (tp40) cc_final: 0.7741 (tt0) REVERT: F 285 ASP cc_start: 0.8182 (m-30) cc_final: 0.7957 (p0) REVERT: G 234 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7258 (tpp80) REVERT: G 235 LEU cc_start: 0.7659 (tp) cc_final: 0.7364 (tt) REVERT: G 285 ASP cc_start: 0.8187 (m-30) cc_final: 0.7868 (p0) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.2388 time to fit residues: 53.4206 Evaluate side-chains 142 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain G residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 0.0570 chunk 46 optimal weight: 0.0570 chunk 136 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN D 76 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13580 Z= 0.143 Angle : 0.459 7.477 18494 Z= 0.221 Chirality : 0.034 0.208 1988 Planarity : 0.003 0.050 2513 Dihedral : 3.106 13.139 1834 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.09 % Allowed : 17.20 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.07 (0.21), residues: 1666 helix: 4.06 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.45 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 156 HIS 0.004 0.001 HIS D 216 PHE 0.013 0.001 PHE C 152 TYR 0.020 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.651 Fit side-chains REVERT: A 198 MET cc_start: 0.8466 (mmt) cc_final: 0.7845 (mmt) REVERT: A 254 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7129 (tt0) REVERT: A 285 ASP cc_start: 0.7988 (m-30) cc_final: 0.7671 (p0) REVERT: B 284 ILE cc_start: 0.9001 (mm) cc_final: 0.8761 (mt) REVERT: C 243 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7301 (ttm170) REVERT: C 255 GLN cc_start: 0.7935 (tp40) cc_final: 0.7623 (tt0) REVERT: E 131 MET cc_start: 0.6767 (mmm) cc_final: 0.6433 (mpp) REVERT: E 235 LEU cc_start: 0.7731 (tp) cc_final: 0.7449 (tt) REVERT: E 252 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8148 (tm-30) REVERT: E 254 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7277 (tt0) REVERT: E 255 GLN cc_start: 0.7686 (tp40) cc_final: 0.7377 (tt0) REVERT: F 73 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8813 (t) REVERT: F 138 ARG cc_start: 0.8437 (tmm-80) cc_final: 0.8136 (tmm160) REVERT: F 198 MET cc_start: 0.8441 (mmt) cc_final: 0.7903 (mmt) REVERT: F 235 LEU cc_start: 0.7642 (tp) cc_final: 0.7321 (tt) REVERT: F 254 GLN cc_start: 0.7965 (tp40) cc_final: 0.7480 (tt0) REVERT: F 285 ASP cc_start: 0.8145 (m-30) cc_final: 0.7937 (p0) REVERT: G 234 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7190 (tpp80) REVERT: G 235 LEU cc_start: 0.7577 (tp) cc_final: 0.7287 (tt) REVERT: G 285 ASP cc_start: 0.8158 (m-30) cc_final: 0.7840 (p0) outliers start: 15 outliers final: 13 residues processed: 150 average time/residue: 0.2643 time to fit residues: 57.8569 Evaluate side-chains 142 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 167 optimal weight: 0.0170 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13580 Z= 0.182 Angle : 0.472 7.636 18494 Z= 0.227 Chirality : 0.035 0.248 1988 Planarity : 0.003 0.062 2513 Dihedral : 3.103 13.228 1834 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.31 % Allowed : 17.13 % Favored : 81.56 % 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: 5.06 (0.21), residues: 1666 helix: 4.07 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.40 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 156 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE E 152 TYR 0.018 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.575 Fit side-chains REVERT: A 198 MET cc_start: 0.8534 (mmt) cc_final: 0.7843 (mmt) REVERT: A 254 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7136 (tt0) REVERT: A 285 ASP cc_start: 0.7916 (m-30) cc_final: 0.7642 (p0) REVERT: B 284 ILE cc_start: 0.9036 (mm) cc_final: 0.8802 (mt) REVERT: C 243 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7281 (ttm170) REVERT: C 255 GLN cc_start: 0.7941 (tp40) cc_final: 0.7635 (tt0) REVERT: E 131 MET cc_start: 0.6781 (mmm) cc_final: 0.6446 (mpp) REVERT: E 235 LEU cc_start: 0.7742 (tp) cc_final: 0.7453 (tt) REVERT: E 252 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 254 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7282 (tt0) REVERT: E 255 GLN cc_start: 0.7740 (tp40) cc_final: 0.7428 (tt0) REVERT: F 73 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8823 (t) REVERT: F 138 ARG cc_start: 0.8441 (tmm-80) cc_final: 0.8073 (ttp-170) REVERT: F 198 MET cc_start: 0.8483 (mmt) cc_final: 0.7911 (mmt) REVERT: F 235 LEU cc_start: 0.7658 (tp) cc_final: 0.7332 (tt) REVERT: F 254 GLN cc_start: 0.7966 (tp40) cc_final: 0.7539 (tt0) REVERT: F 285 ASP cc_start: 0.8143 (m-30) cc_final: 0.7936 (p0) REVERT: G 234 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7199 (tpp80) REVERT: G 235 LEU cc_start: 0.7582 (tp) cc_final: 0.7295 (tt) REVERT: G 285 ASP cc_start: 0.8119 (m-30) cc_final: 0.7808 (p0) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.2483 time to fit residues: 52.8005 Evaluate side-chains 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.086233 restraints weight = 16688.687| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.66 r_work: 0.2724 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 13580 Z= 0.202 Angle : 0.718 59.200 18494 Z= 0.406 Chirality : 0.035 0.313 1988 Planarity : 0.003 0.061 2513 Dihedral : 3.129 14.894 1834 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.17 % Allowed : 17.13 % Favored : 81.71 % Cbeta Deviations : 0.06 % 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: 5.05 (0.21), residues: 1666 helix: 4.06 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.40 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 156 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE E 152 TYR 0.017 0.001 TYR G 226 ARG 0.005 0.000 ARG E 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.03 seconds wall clock time: 48 minutes 59.49 seconds (2939.49 seconds total)