Starting phenix.real_space_refine on Sun Apr 5 20:26:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.map" model { file = "/net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dyr_30923/04_2026/7dyr_30923.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 81 5.16 5 C 8667 2.51 5 N 2229 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "Z" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "G" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.23 Number of scatterers: 13326 At special positions: 0 Unit cell: (120.954, 128.381, 85.941, 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 81 16.00 O 2349 8.00 N 2229 7.00 C 8667 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 626.3 milliseconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 3 sheets defined 77.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 117 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP Y 129 " --> pdb=" O ASP Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL Y 151 " --> pdb=" O GLN Y 147 " (cutoff:3.500A) Proline residue: Y 154 - end of helix removed outlier: 3.808A pdb=" N ALA Y 159 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 171 removed outlier: 3.727A pdb=" N ASN Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL Y 191 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 Processing helix chain 'Z' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O GLN Z 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Z 24 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 99 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.512A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 183 No H-bonds generated for 'chain 'Z' and resid 181 through 183' Processing helix chain 'Z' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR Z 211 " --> pdb=" O VAL Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 242 Processing helix chain 'Z' and resid 244 through 260 Processing helix chain 'Z' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.543A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.808A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 192 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.595A pdb=" N HIS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.512A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.869A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.808A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 192 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG F 22 " --> pdb=" O GLN F 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.716A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.512A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 244 through 260 Processing helix chain 'F' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR Z 232 " --> pdb=" O VAL Z 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR C 232 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR F 232 " --> pdb=" O VAL F 219 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2664 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: 1.93 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 2665 1.46 - 1.58: 6509 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 13590 Sorted by residual: bond pdb=" N GLN F 41 " pdb=" CA GLN F 41 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.59e+00 bond pdb=" N GLN C 41 " pdb=" CA GLN C 41 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" CB PRO Z 132 " pdb=" CG PRO Z 132 " ideal model delta sigma weight residual 1.492 1.406 0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.92e+00 bond pdb=" CB PRO F 132 " pdb=" CG PRO F 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.91e+00 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17977 1.97 - 3.94: 413 3.94 - 5.91: 83 5.91 - 7.89: 16 7.89 - 9.86: 9 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N VAL E 156 " pdb=" CA VAL E 156 " pdb=" C VAL E 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL Y 156 " pdb=" CA VAL Y 156 " pdb=" C VAL Y 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL B 156 " pdb=" CA VAL B 156 " pdb=" C VAL B 156 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" C GLN Z 41 " pdb=" CA GLN Z 41 " pdb=" CB GLN Z 41 " ideal model delta sigma weight residual 111.48 105.78 5.70 1.59e+00 3.96e-01 1.29e+01 angle pdb=" CA TYR A 73 " pdb=" CB TYR A 73 " pdb=" CG TYR A 73 " ideal model delta sigma weight residual 113.90 107.46 6.44 1.80e+00 3.09e-01 1.28e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7076 17.78 - 35.56: 650 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7953 sinusoidal: 2979 harmonic: 4974 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N PRO B 175 " pdb=" CA PRO B 175 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE Y 174 " pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1715 0.052 - 0.104: 424 0.104 - 0.157: 78 0.157 - 0.209: 8 0.209 - 0.261: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CA ASP Z 103 " pdb=" N ASP Z 103 " pdb=" C ASP Z 103 " pdb=" CB ASP Z 103 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2223 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Y 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 71 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 72 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.050 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2180 2.74 - 3.28: 13533 3.28 - 3.82: 22248 3.82 - 4.36: 26647 4.36 - 4.90: 46236 Nonbonded interactions: 110844 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 125 " pdb=" NH2 ARG Z 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP E 125 " pdb=" NH2 ARG F 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP B 125 " pdb=" NH2 ARG C 39 " model vdw 2.206 3.120 nonbonded pdb=" N ASN G 67 " pdb=" OD1 ASN G 67 " model vdw 2.275 3.120 nonbonded pdb=" N ASN D 67 " pdb=" OD1 ASN D 67 " model vdw 2.275 3.120 ... (remaining 110839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'Y' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'Z' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'D' 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: 4.140 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 : 0.008 0.086 13590 Z= 0.325 Angle : 0.779 9.857 18498 Z= 0.420 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.368 88.905 4797 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 3.56 % Allowed : 20.33 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 54 TYR 0.027 0.003 TYR A 73 PHE 0.011 0.001 PHE C 47 TRP 0.011 0.001 TRP E 138 HIS 0.004 0.001 HIS Y 122 Details of bonding type rmsd covalent geometry : bond 0.00776 (13590) covalent geometry : angle 0.77939 (18498) hydrogen bonds : bond 0.14245 ( 888) hydrogen bonds : angle 5.94953 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.463 Fit side-chains REVERT: Y 26 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Y 64 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: Y 125 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: Y 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tm-30) REVERT: Z 17 THR cc_start: 0.7504 (m) cc_final: 0.7291 (p) REVERT: Z 38 GLU cc_start: 0.8653 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 60 ASN cc_start: 0.6699 (m-40) cc_final: 0.6131 (t0) REVERT: Z 73 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6989 (mt-10) REVERT: Z 94 GLU cc_start: 0.7693 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 175 LYS cc_start: 0.7153 (tptm) cc_final: 0.6931 (tptp) REVERT: Z 223 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7239 (m) REVERT: Z 230 HIS cc_start: 0.7483 (m90) cc_final: 0.7028 (m90) REVERT: A 50 ASP cc_start: 0.6889 (m-30) cc_final: 0.6620 (m-30) REVERT: A 55 ASN cc_start: 0.8150 (p0) cc_final: 0.7944 (p0) REVERT: B 26 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 64 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 125 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (m-30) REVERT: B 201 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtp) REVERT: C 15 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7833 (ptpp) REVERT: C 17 THR cc_start: 0.7845 (m) cc_final: 0.7635 (p) REVERT: C 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7260 (m-30) REVERT: C 22 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6116 (mtm110) REVERT: C 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8073 (tt0) REVERT: C 60 ASN cc_start: 0.6867 (m-40) cc_final: 0.6507 (t0) REVERT: C 73 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 50 ASP cc_start: 0.7159 (m-30) cc_final: 0.6647 (m-30) REVERT: D 55 ASN cc_start: 0.8316 (p0) cc_final: 0.7979 (p0) REVERT: E 3 ILE cc_start: 0.7863 (mt) cc_final: 0.7514 (mm) REVERT: E 4 THR cc_start: 0.7488 (p) cc_final: 0.7264 (t) REVERT: E 130 ASN cc_start: 0.8118 (m110) cc_final: 0.7796 (m-40) REVERT: E 142 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 176 GLU cc_start: 0.7063 (tp30) cc_final: 0.6785 (tm-30) REVERT: E 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7495 (m-40) REVERT: E 244 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7980 (ttpp) REVERT: F 17 THR cc_start: 0.7743 (m) cc_final: 0.7460 (p) REVERT: F 38 GLU cc_start: 0.8654 (tt0) cc_final: 0.8036 (tt0) REVERT: F 60 ASN cc_start: 0.6881 (m-40) cc_final: 0.6221 (t0) REVERT: F 73 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 95 GLN cc_start: 0.7180 (mp10) cc_final: 0.6768 (mp-120) REVERT: F 102 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6931 (mm) REVERT: F 108 ASN cc_start: 0.7986 (m-40) cc_final: 0.7752 (m-40) REVERT: F 189 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: F 193 GLU cc_start: 0.7609 (tt0) cc_final: 0.7397 (tt0) REVERT: F 259 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6457 (ttp80) REVERT: F 281 CYS cc_start: 0.7790 (m) cc_final: 0.7579 (m) REVERT: G 19 TRP cc_start: 0.6334 (t60) cc_final: 0.6107 (t60) outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 0.5540 time to fit residues: 191.8820 Evaluate side-chains 241 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 MET Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 29 ASN A 15 ASN A 42 GLN C 108 ASN C 158 ASN D 15 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.076192 restraints weight = 17965.476| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.68 r_work: 0.2877 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13590 Z= 0.168 Angle : 0.626 6.518 18498 Z= 0.332 Chirality : 0.043 0.175 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.910 55.910 1970 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Rotamer: Outliers : 3.70 % Allowed : 17.28 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.21), residues: 1773 helix: 1.28 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 96 TYR 0.026 0.002 TYR A 73 PHE 0.014 0.001 PHE C 157 TRP 0.010 0.001 TRP C 127 HIS 0.003 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00385 (13590) covalent geometry : angle 0.62649 (18498) hydrogen bonds : bond 0.05260 ( 888) hydrogen bonds : angle 4.26572 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: Z 60 ASN cc_start: 0.7184 (m-40) cc_final: 0.6818 (t0) REVERT: Z 94 GLU cc_start: 0.8846 (tt0) cc_final: 0.8465 (tt0) REVERT: Z 223 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7480 (m) REVERT: Z 230 HIS cc_start: 0.8010 (m90) cc_final: 0.7734 (m90) REVERT: B 26 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8291 (mm-30) REVERT: C 17 THR cc_start: 0.8734 (m) cc_final: 0.8488 (p) REVERT: C 20 ASP cc_start: 0.8753 (m-30) cc_final: 0.8518 (m-30) REVERT: C 38 GLU cc_start: 0.9030 (tt0) cc_final: 0.8775 (tt0) REVERT: C 60 ASN cc_start: 0.7214 (m-40) cc_final: 0.7001 (t0) REVERT: D 16 ASN cc_start: 0.8277 (m-40) cc_final: 0.8053 (m-40) REVERT: E 176 GLU cc_start: 0.7353 (tp30) cc_final: 0.6964 (tm-30) REVERT: F 38 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8831 (tt0) REVERT: F 95 GLN cc_start: 0.8423 (mp10) cc_final: 0.8081 (mp-120) REVERT: F 183 MET cc_start: 0.6535 (mmm) cc_final: 0.6289 (mmm) REVERT: F 189 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: G 19 TRP cc_start: 0.6742 (t60) cc_final: 0.6426 (t60) outliers start: 51 outliers final: 18 residues processed: 271 average time/residue: 0.5628 time to fit residues: 166.3077 Evaluate side-chains 235 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 126 LYS Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 0.0010 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 29 ASN F 108 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.075104 restraints weight = 18065.189| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.69 r_work: 0.2855 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.171 Angle : 0.609 7.274 18498 Z= 0.323 Chirality : 0.043 0.179 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.452 59.629 1954 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.74 % Rotamer: Outliers : 3.27 % Allowed : 17.50 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1773 helix: 1.39 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.027 0.002 TYR A 73 PHE 0.012 0.001 PHE F 47 TRP 0.010 0.001 TRP Z 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00401 (13590) covalent geometry : angle 0.60909 (18498) hydrogen bonds : bond 0.05285 ( 888) hydrogen bonds : angle 4.12613 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: Y 176 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: Z 94 GLU cc_start: 0.8830 (tt0) cc_final: 0.8478 (tt0) REVERT: Z 223 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7451 (m) REVERT: Z 230 HIS cc_start: 0.7986 (m90) cc_final: 0.7708 (m90) REVERT: B 26 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 64 MET cc_start: 0.9412 (ptp) cc_final: 0.9169 (ptp) REVERT: C 38 GLU cc_start: 0.9037 (tt0) cc_final: 0.8792 (tt0) REVERT: D 16 ASN cc_start: 0.8242 (m-40) cc_final: 0.8019 (m-40) REVERT: D 29 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5902 (tm) REVERT: E 64 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: E 176 GLU cc_start: 0.7262 (tp30) cc_final: 0.6932 (tm-30) REVERT: F 38 GLU cc_start: 0.9141 (tt0) cc_final: 0.8888 (tt0) REVERT: F 95 GLN cc_start: 0.8418 (mp10) cc_final: 0.8068 (mp-120) REVERT: F 183 MET cc_start: 0.6694 (mmm) cc_final: 0.6412 (mmm) REVERT: F 189 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: G 19 TRP cc_start: 0.6740 (t60) cc_final: 0.6413 (t60) outliers start: 45 outliers final: 21 residues processed: 268 average time/residue: 0.5692 time to fit residues: 166.2786 Evaluate side-chains 250 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 176 GLU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 138 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 7 GLN Z 60 ASN A 15 ASN A 42 GLN B 180 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 108 ASN F 189 GLN G 11 ASN G 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075766 restraints weight = 18016.067| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.69 r_work: 0.2867 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.157 Angle : 0.590 6.751 18498 Z= 0.313 Chirality : 0.042 0.173 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.465 57.486 1954 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.15 % Favored : 93.68 % Rotamer: Outliers : 2.98 % Allowed : 18.37 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1773 helix: 1.56 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 64 TYR 0.026 0.002 TYR A 73 PHE 0.012 0.001 PHE F 47 TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00363 (13590) covalent geometry : angle 0.58969 (18498) hydrogen bonds : bond 0.04926 ( 888) hydrogen bonds : angle 4.01362 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: Y 58 MET cc_start: 0.9104 (mmm) cc_final: 0.8502 (mmp) REVERT: Y 125 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: Z 60 ASN cc_start: 0.6961 (m-40) cc_final: 0.6491 (t0) REVERT: Z 223 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7415 (m) REVERT: Z 230 HIS cc_start: 0.7970 (m90) cc_final: 0.7670 (m90) REVERT: A 16 ASN cc_start: 0.8123 (m-40) cc_final: 0.7915 (m-40) REVERT: B 26 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 64 MET cc_start: 0.9429 (ptp) cc_final: 0.8804 (ptp) REVERT: B 166 GLU cc_start: 0.6628 (pm20) cc_final: 0.6346 (pm20) REVERT: C 38 GLU cc_start: 0.9031 (tt0) cc_final: 0.8822 (tt0) REVERT: D 16 ASN cc_start: 0.8182 (m-40) cc_final: 0.7951 (m-40) REVERT: D 29 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6227 (tm) REVERT: E 64 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8723 (mtp) REVERT: F 38 GLU cc_start: 0.9112 (tt0) cc_final: 0.8875 (tt0) REVERT: F 95 GLN cc_start: 0.8421 (mp10) cc_final: 0.8044 (mp-120) REVERT: F 183 MET cc_start: 0.6697 (mmm) cc_final: 0.6413 (mmm) REVERT: F 189 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: G 19 TRP cc_start: 0.6800 (t60) cc_final: 0.6434 (t60) outliers start: 41 outliers final: 20 residues processed: 260 average time/residue: 0.5592 time to fit residues: 158.8005 Evaluate side-chains 243 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 157 optimal weight: 0.0270 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 7 GLN A 15 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076022 restraints weight = 18078.754| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.69 r_work: 0.2870 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13590 Z= 0.152 Angle : 0.582 7.959 18498 Z= 0.309 Chirality : 0.042 0.170 2226 Planarity : 0.006 0.087 2328 Dihedral : 5.421 57.097 1954 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 3.12 % Allowed : 18.45 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1773 helix: 1.69 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.43 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.025 0.002 TYR A 73 PHE 0.013 0.001 PHE F 47 TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00352 (13590) covalent geometry : angle 0.58197 (18498) hydrogen bonds : bond 0.04856 ( 888) hydrogen bonds : angle 3.95596 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8214 (mtmt) REVERT: Y 58 MET cc_start: 0.9126 (mmm) cc_final: 0.8598 (mmp) REVERT: Y 125 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: Z 187 PHE cc_start: 0.8153 (t80) cc_final: 0.7907 (t80) REVERT: Z 223 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7398 (m) REVERT: Z 230 HIS cc_start: 0.8010 (m90) cc_final: 0.7675 (m90) REVERT: A 16 ASN cc_start: 0.8167 (m-40) cc_final: 0.7955 (m-40) REVERT: A 29 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6114 (tm) REVERT: B 26 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8224 (mm-30) REVERT: B 47 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8306 (tttp) REVERT: B 64 MET cc_start: 0.9445 (ptp) cc_final: 0.8898 (ptp) REVERT: B 244 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: C 38 GLU cc_start: 0.9016 (tt0) cc_final: 0.8803 (tt0) REVERT: D 16 ASN cc_start: 0.8169 (m-40) cc_final: 0.7923 (m-40) REVERT: D 29 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6116 (tm) REVERT: E 64 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: F 38 GLU cc_start: 0.9071 (tt0) cc_final: 0.8869 (tt0) REVERT: F 95 GLN cc_start: 0.8413 (mp10) cc_final: 0.8134 (mp-120) REVERT: F 183 MET cc_start: 0.6665 (mmm) cc_final: 0.6406 (mmm) REVERT: F 189 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: G 19 TRP cc_start: 0.6842 (t60) cc_final: 0.6468 (t60) outliers start: 43 outliers final: 20 residues processed: 261 average time/residue: 0.5544 time to fit residues: 158.1185 Evaluate side-chains 250 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 160 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 7 GLN Z 60 ASN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.075373 restraints weight = 17938.177| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.69 r_work: 0.2858 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13590 Z= 0.162 Angle : 0.599 10.280 18498 Z= 0.317 Chirality : 0.042 0.172 2226 Planarity : 0.006 0.085 2328 Dihedral : 5.434 56.422 1954 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.34 % Allowed : 18.30 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1773 helix: 1.75 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.39 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 39 TYR 0.026 0.002 TYR A 73 PHE 0.014 0.001 PHE F 47 TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00378 (13590) covalent geometry : angle 0.59933 (18498) hydrogen bonds : bond 0.04995 ( 888) hydrogen bonds : angle 3.96539 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8296 (mtmt) REVERT: Y 125 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: Y 244 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8547 (ttpp) REVERT: Z 60 ASN cc_start: 0.7030 (m-40) cc_final: 0.6522 (t0) REVERT: Z 187 PHE cc_start: 0.8151 (t80) cc_final: 0.7898 (t80) REVERT: Z 223 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7420 (m) REVERT: Z 230 HIS cc_start: 0.7996 (m90) cc_final: 0.7654 (m90) REVERT: A 16 ASN cc_start: 0.8162 (m-40) cc_final: 0.7924 (m-40) REVERT: A 29 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6278 (tm) REVERT: B 26 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 47 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8301 (tttp) REVERT: B 64 MET cc_start: 0.9427 (ptp) cc_final: 0.8760 (ptp) REVERT: C 38 GLU cc_start: 0.9041 (tt0) cc_final: 0.8828 (tt0) REVERT: D 16 ASN cc_start: 0.8131 (m-40) cc_final: 0.7823 (m-40) REVERT: D 29 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6111 (tm) REVERT: E 47 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8515 (tttt) REVERT: E 64 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8688 (mtp) REVERT: F 95 GLN cc_start: 0.8404 (mp10) cc_final: 0.8040 (mp-120) REVERT: F 183 MET cc_start: 0.6672 (mmm) cc_final: 0.6410 (mmm) REVERT: F 189 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: G 19 TRP cc_start: 0.6873 (t60) cc_final: 0.6459 (t60) outliers start: 46 outliers final: 26 residues processed: 264 average time/residue: 0.5547 time to fit residues: 159.8710 Evaluate side-chains 252 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 174 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 33 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 148 optimal weight: 0.3980 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 7 GLN A 15 ASN A 74 ASN C 71 HIS C 108 ASN D 11 ASN D 15 ASN E 121 GLN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.078514 restraints weight = 18085.038| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.68 r_work: 0.2915 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13590 Z= 0.127 Angle : 0.549 9.005 18498 Z= 0.291 Chirality : 0.040 0.149 2226 Planarity : 0.005 0.085 2328 Dihedral : 5.307 59.934 1954 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.83 % Allowed : 18.81 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1773 helix: 1.95 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.018 0.001 TYR D 73 PHE 0.012 0.001 PHE F 47 TRP 0.009 0.001 TRP Y 138 HIS 0.002 0.000 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00276 (13590) covalent geometry : angle 0.54948 (18498) hydrogen bonds : bond 0.04245 ( 888) hydrogen bonds : angle 3.82831 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (mtmt) REVERT: Y 58 MET cc_start: 0.9041 (mmm) cc_final: 0.8674 (mmp) REVERT: Y 125 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: Y 244 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8344 (ttpp) REVERT: Z 187 PHE cc_start: 0.8101 (t80) cc_final: 0.7880 (t80) REVERT: Z 223 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7397 (m) REVERT: Z 230 HIS cc_start: 0.7996 (m90) cc_final: 0.7619 (m90) REVERT: A 16 ASN cc_start: 0.8152 (m-40) cc_final: 0.7865 (m-40) REVERT: B 26 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 47 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8303 (tttp) REVERT: B 64 MET cc_start: 0.9386 (ptp) cc_final: 0.8603 (ptp) REVERT: B 172 ASN cc_start: 0.6386 (m-40) cc_final: 0.6142 (m-40) REVERT: C 61 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6845 (p0) REVERT: D 16 ASN cc_start: 0.8132 (m-40) cc_final: 0.7878 (m-40) REVERT: D 29 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6173 (tm) REVERT: D 74 ASN cc_start: 0.8185 (t0) cc_final: 0.7950 (t0) REVERT: E 176 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: F 95 GLN cc_start: 0.8414 (mp10) cc_final: 0.8081 (mp-120) REVERT: F 183 MET cc_start: 0.6659 (mmm) cc_final: 0.6383 (mmm) REVERT: F 189 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: G 19 TRP cc_start: 0.6868 (t60) cc_final: 0.6474 (t60) outliers start: 39 outliers final: 22 residues processed: 266 average time/residue: 0.5588 time to fit residues: 163.2005 Evaluate side-chains 258 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 174 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 3.9990 chunk 161 optimal weight: 0.0570 chunk 145 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.0770 chunk 156 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.0370 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 121 GLN Z 36 ASN A 15 ASN B 130 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.078946 restraints weight = 17967.205| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.69 r_work: 0.2925 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13590 Z= 0.125 Angle : 0.548 10.181 18498 Z= 0.289 Chirality : 0.040 0.145 2226 Planarity : 0.005 0.081 2328 Dihedral : 5.213 58.599 1954 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 18.74 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1773 helix: 2.06 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -2.33 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.017 0.001 TYR D 73 PHE 0.012 0.001 PHE F 47 TRP 0.009 0.001 TRP F 127 HIS 0.002 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00271 (13590) covalent geometry : angle 0.54847 (18498) hydrogen bonds : bond 0.04136 ( 888) hydrogen bonds : angle 3.78364 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8309 (mtmt) REVERT: Y 58 MET cc_start: 0.9024 (mmm) cc_final: 0.8620 (mmp) REVERT: Y 125 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: Y 244 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8300 (ttpp) REVERT: Z 61 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.7035 (p0) REVERT: Z 187 PHE cc_start: 0.8096 (t80) cc_final: 0.7870 (t80) REVERT: Z 223 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7416 (m) REVERT: Z 230 HIS cc_start: 0.7997 (m90) cc_final: 0.7607 (m90) REVERT: A 16 ASN cc_start: 0.8130 (m-40) cc_final: 0.7833 (m110) REVERT: A 29 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6138 (tm) REVERT: B 26 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 47 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8296 (tttp) REVERT: B 64 MET cc_start: 0.9385 (ptp) cc_final: 0.8605 (ptp) REVERT: B 172 ASN cc_start: 0.6346 (m-40) cc_final: 0.6135 (m-40) REVERT: C 61 ASN cc_start: 0.7095 (OUTLIER) cc_final: 0.6815 (p0) REVERT: D 16 ASN cc_start: 0.8123 (m-40) cc_final: 0.7861 (m-40) REVERT: D 29 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6161 (tm) REVERT: F 36 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8248 (p0) REVERT: F 95 GLN cc_start: 0.8410 (mp10) cc_final: 0.8081 (mp-120) REVERT: F 183 MET cc_start: 0.6664 (mmm) cc_final: 0.6391 (mmm) REVERT: F 189 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: G 19 TRP cc_start: 0.6859 (t60) cc_final: 0.6462 (t60) outliers start: 42 outliers final: 25 residues processed: 264 average time/residue: 0.5511 time to fit residues: 158.9177 Evaluate side-chains 259 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 4 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 164 optimal weight: 0.0470 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076796 restraints weight = 18114.747| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.70 r_work: 0.2884 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13590 Z= 0.148 Angle : 0.587 10.635 18498 Z= 0.310 Chirality : 0.041 0.168 2226 Planarity : 0.005 0.076 2328 Dihedral : 5.250 59.521 1954 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.15 % Favored : 93.68 % Rotamer: Outliers : 3.12 % Allowed : 18.95 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.21), residues: 1773 helix: 2.00 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 64 TYR 0.025 0.002 TYR D 73 PHE 0.014 0.001 PHE F 47 TRP 0.010 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00341 (13590) covalent geometry : angle 0.58733 (18498) hydrogen bonds : bond 0.04600 ( 888) hydrogen bonds : angle 3.82811 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: Y 58 MET cc_start: 0.9063 (mmm) cc_final: 0.8622 (mmp) REVERT: Y 244 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8473 (ttpp) REVERT: Z 36 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.7725 (p0) REVERT: Z 61 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.7018 (p0) REVERT: Z 187 PHE cc_start: 0.8133 (t80) cc_final: 0.7913 (t80) REVERT: Z 223 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7388 (m) REVERT: Z 230 HIS cc_start: 0.7992 (m90) cc_final: 0.7610 (m90) REVERT: A 16 ASN cc_start: 0.8171 (m-40) cc_final: 0.7880 (m110) REVERT: A 29 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6199 (tm) REVERT: B 26 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8204 (mm-30) REVERT: B 47 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8274 (tttp) REVERT: B 64 MET cc_start: 0.9417 (ptp) cc_final: 0.8660 (ptp) REVERT: B 172 ASN cc_start: 0.6362 (m-40) cc_final: 0.5928 (m-40) REVERT: C 61 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6835 (p0) REVERT: D 16 ASN cc_start: 0.8109 (m-40) cc_final: 0.7798 (m-40) REVERT: D 29 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6198 (tm) REVERT: F 36 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8255 (p0) REVERT: F 95 GLN cc_start: 0.8402 (mp10) cc_final: 0.8068 (mp-120) REVERT: F 183 MET cc_start: 0.6649 (mmm) cc_final: 0.6380 (mmm) REVERT: F 189 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: G 19 TRP cc_start: 0.6826 (t60) cc_final: 0.6407 (t60) outliers start: 43 outliers final: 19 residues processed: 256 average time/residue: 0.5626 time to fit residues: 157.1328 Evaluate side-chains 248 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 30 optimal weight: 0.4980 chunk 64 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 146 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 189 GLN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078792 restraints weight = 17984.001| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.67 r_work: 0.2919 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13590 Z= 0.129 Angle : 0.571 11.357 18498 Z= 0.300 Chirality : 0.040 0.147 2226 Planarity : 0.005 0.076 2328 Dihedral : 4.986 57.674 1952 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 2.61 % Allowed : 19.61 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1773 helix: 2.06 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 221 TYR 0.018 0.001 TYR D 73 PHE 0.011 0.001 PHE F 47 TRP 0.011 0.001 TRP Y 138 HIS 0.002 0.000 HIS Y 122 Details of bonding type rmsd covalent geometry : bond 0.00281 (13590) covalent geometry : angle 0.57133 (18498) hydrogen bonds : bond 0.04206 ( 888) hydrogen bonds : angle 3.77724 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8347 (mtmt) REVERT: Y 58 MET cc_start: 0.9039 (mmm) cc_final: 0.8622 (mmp) REVERT: Y 244 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8301 (ttpp) REVERT: Z 36 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.7721 (p0) REVERT: Z 61 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6927 (p0) REVERT: Z 187 PHE cc_start: 0.8101 (t80) cc_final: 0.7871 (t80) REVERT: Z 223 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7395 (m) REVERT: Z 230 HIS cc_start: 0.8000 (m90) cc_final: 0.7581 (m90) REVERT: A 16 ASN cc_start: 0.8159 (m-40) cc_final: 0.7856 (m110) REVERT: A 29 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6147 (tm) REVERT: B 26 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8144 (mm-30) REVERT: B 47 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8300 (tttp) REVERT: B 64 MET cc_start: 0.9383 (ptp) cc_final: 0.8727 (ptp) REVERT: C 61 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6741 (p0) REVERT: D 16 ASN cc_start: 0.8138 (m-40) cc_final: 0.7860 (m-40) REVERT: D 29 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6050 (tm) REVERT: F 95 GLN cc_start: 0.8402 (mp10) cc_final: 0.8136 (mp-120) REVERT: F 183 MET cc_start: 0.6679 (mmm) cc_final: 0.6444 (mmm) REVERT: F 189 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: G 19 TRP cc_start: 0.6838 (t60) cc_final: 0.6414 (t60) outliers start: 36 outliers final: 19 residues processed: 256 average time/residue: 0.5599 time to fit residues: 156.9998 Evaluate side-chains 249 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 169 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.0170 chunk 54 optimal weight: 0.7980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 ASN Z 189 GLN A 15 ASN C 98 ASN C 108 ASN D 15 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.078040 restraints weight = 18055.225| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.69 r_work: 0.2906 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13590 Z= 0.135 Angle : 0.578 11.497 18498 Z= 0.304 Chirality : 0.041 0.157 2226 Planarity : 0.005 0.074 2328 Dihedral : 4.899 56.388 1951 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 2.83 % Allowed : 19.32 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1773 helix: 2.06 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 39 TYR 0.021 0.001 TYR D 73 PHE 0.012 0.001 PHE F 47 TRP 0.010 0.001 TRP Y 138 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00303 (13590) covalent geometry : angle 0.57844 (18498) hydrogen bonds : bond 0.04333 ( 888) hydrogen bonds : angle 3.78252 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5616.74 seconds wall clock time: 95 minutes 54.85 seconds (5754.85 seconds total)