Starting phenix.real_space_refine on Sun Dec 10 03:24:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/12_2023/6xzc_10658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/12_2023/6xzc_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_10658/12_2023/6xzc_10658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/12_2023/6xzc_10658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/12_2023/6xzc_10658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/12_2023/6xzc_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-1.21rc1-5172/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: 6.93, per 1000 atoms: 0.52 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: 4.78 Conformation dependent library (CDL) restraints added in 2.4 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: 1.06 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: 3.62 Time building geometry restraints manager: 5.26 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 13.930 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.630 Find NCS groups from input model: 0.830 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.920 ------------------------------------------------------------------------------- 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 : 1.520 Fit side-chains outliers start: 42 outliers final: 1 residues processed: 357 average time/residue: 0.2707 time to fit residues: 135.6764 Evaluate side-chains 177 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1125 time to fit residues: 2.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 0.7980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13580 Z= 0.219 Angle : 0.540 6.321 18494 Z= 0.281 Chirality : 0.034 0.146 1988 Planarity : 0.005 0.056 2513 Dihedral : 3.520 14.022 1834 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.17 % Allowed : 13.19 % Favored : 85.64 % 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: 1.99 (0.20), residues: 1666 helix: 1.87 (0.13), residues: 1204 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.010 0.001 HIS B 151 PHE 0.017 0.002 PHE A 152 TYR 0.032 0.002 TYR A 226 ARG 0.005 0.000 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 206 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.518 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 201 average time/residue: 0.2277 time to fit residues: 69.4223 Evaluate side-chains 163 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1160 time to fit residues: 3.6252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN F 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13580 Z= 0.202 Angle : 0.497 7.524 18494 Z= 0.246 Chirality : 0.033 0.166 1988 Planarity : 0.004 0.042 2513 Dihedral : 3.309 13.414 1834 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.58 % Allowed : 15.60 % Favored : 83.82 % 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: 3.27 (0.20), residues: 1666 helix: 2.74 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 0.57 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 156 HIS 0.012 0.001 HIS B 151 PHE 0.018 0.002 PHE B 152 TYR 0.023 0.001 TYR G 226 ARG 0.005 0.000 ARG D 57 *********************** 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 171 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.599 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 168 average time/residue: 0.2479 time to fit residues: 61.5248 Evaluate side-chains 141 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4053 time to fit residues: 3.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 48 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 245 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN G 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13580 Z= 0.229 Angle : 0.522 8.206 18494 Z= 0.258 Chirality : 0.036 0.223 1988 Planarity : 0.004 0.064 2513 Dihedral : 3.337 13.598 1834 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.60 % Allowed : 15.45 % Favored : 82.94 % 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: 4.06 (0.21), residues: 1666 helix: 3.30 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.11 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 156 HIS 0.004 0.001 HIS D 216 PHE 0.019 0.002 PHE D 152 TYR 0.023 0.002 TYR A 253 ARG 0.009 0.001 ARG G 234 *********************** 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 183 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.494 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 176 average time/residue: 0.2658 time to fit residues: 69.0736 Evaluate side-chains 155 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1202 time to fit residues: 5.8605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 245 GLN D 175 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13580 Z= 0.182 Angle : 0.472 8.093 18494 Z= 0.228 Chirality : 0.034 0.210 1988 Planarity : 0.003 0.028 2513 Dihedral : 3.207 12.507 1834 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.87 % Allowed : 15.67 % Favored : 83.45 % 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: 4.53 (0.21), residues: 1666 helix: 3.65 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.27 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 156 HIS 0.005 0.001 HIS D 216 PHE 0.017 0.002 PHE D 152 TYR 0.020 0.001 TYR G 226 ARG 0.005 0.000 ARG A 243 *********************** 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 158 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.532 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 155 average time/residue: 0.2470 time to fit residues: 57.4456 Evaluate side-chains 128 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1208 time to fit residues: 3.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 D 12 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 254 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6042 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= 0.165 Angle : 0.468 7.248 18494 Z= 0.224 Chirality : 0.035 0.221 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.133 12.625 1834 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.73 % Allowed : 17.20 % Favored : 82.07 % 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: 4.77 (0.21), residues: 1666 helix: 3.84 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.35 (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 0.016 0.001 PHE D 152 TYR 0.017 0.001 TYR G 226 ARG 0.005 0.000 ARG C 220 *********************** 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 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.525 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.2503 time to fit residues: 52.1417 Evaluate side-chains 125 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1176 time to fit residues: 2.9301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 0.0370 chunk 74 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6282 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 : 0.469 7.231 18494 Z= 0.224 Chirality : 0.034 0.219 1988 Planarity : 0.003 0.029 2513 Dihedral : 3.107 13.387 1834 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.44 % Allowed : 17.27 % Favored : 82.29 % 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: 4.88 (0.21), residues: 1666 helix: 3.92 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.38 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.005 0.001 HIS D 216 PHE 0.015 0.001 PHE D 152 TYR 0.016 0.001 TYR G 226 ARG 0.006 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 135 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.404 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 134 average time/residue: 0.2562 time to fit residues: 50.8673 Evaluate side-chains 122 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1569 time to fit residues: 2.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 147 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN D 216 HIS F 48 GLN G 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13580 Z= 0.214 Angle : 0.493 7.797 18494 Z= 0.238 Chirality : 0.036 0.237 1988 Planarity : 0.003 0.034 2513 Dihedral : 3.177 13.348 1834 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.66 % Allowed : 17.06 % Favored : 82.29 % 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: 4.85 (0.21), residues: 1666 helix: 3.90 (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 0.009 0.001 TRP F 156 HIS 0.005 0.001 HIS C 216 PHE 0.015 0.002 PHE D 152 TYR 0.014 0.001 TYR G 226 ARG 0.007 0.000 ARG G 221 *********************** 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 138 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.509 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 136 average time/residue: 0.2600 time to fit residues: 52.7778 Evaluate side-chains 124 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1177 time to fit residues: 2.2444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 0.0370 chunk 46 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 48 GLN D 76 ASN G 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13580 Z= 0.177 Angle : 0.487 7.597 18494 Z= 0.233 Chirality : 0.036 0.244 1988 Planarity : 0.003 0.053 2513 Dihedral : 3.133 13.933 1834 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.44 % Allowed : 17.35 % 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: 5.00 (0.21), residues: 1666 helix: 4.00 (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 E 156 HIS 0.004 0.001 HIS D 216 PHE 0.014 0.001 PHE D 152 TYR 0.016 0.001 TYR G 226 ARG 0.007 0.000 ARG A 243 *********************** 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 130 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.708 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.2592 time to fit residues: 49.7004 Evaluate side-chains 119 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 2.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN F 48 GLN G 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.003 0.031 13580 Z= 0.173 Angle : 0.487 7.702 18494 Z= 0.231 Chirality : 0.035 0.249 1988 Planarity : 0.003 0.061 2513 Dihedral : 3.101 12.948 1834 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.36 % Allowed : 17.20 % Favored : 82.43 % 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: 5.09 (0.21), residues: 1666 helix: 4.07 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.48 (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 C 216 PHE 0.013 0.001 PHE D 152 TYR 0.011 0.001 TYR A 226 ARG 0.007 0.000 ARG A 243 ********************** 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 125 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.553 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.2667 time to fit residues: 48.7399 Evaluate side-chains 118 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1351 time to fit residues: 2.9692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 48 GLN G 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.088604 restraints weight = 16626.730| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.69 r_work: 0.2752 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13580 Z= 0.151 Angle : 0.479 7.624 18494 Z= 0.225 Chirality : 0.035 0.236 1988 Planarity : 0.003 0.056 2513 Dihedral : 3.054 13.550 1834 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.15 % Allowed : 17.42 % Favored : 82.43 % 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: 5.22 (0.21), residues: 1666 helix: 4.17 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.51 (0.34), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.003 0.001 HIS B 216 PHE 0.013 0.001 PHE C 152 TYR 0.012 0.001 TYR A 226 ARG 0.006 0.000 ARG G 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.12 seconds wall clock time: 48 minutes 52.66 seconds (2932.66 seconds total)