Starting phenix.real_space_refine on Thu Aug 6 20:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr9_60393/08_2026/8zr9_60393.map" } resolution = 2.7 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= 0.004 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 72 5.16 5 C 10638 2.51 5 N 2814 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16692 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "B" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "C" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "D" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "E" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'4BW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.25 Number of scatterers: 16692 At special positions: 0 Unit cell: (85.744, 84.812, 169.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 12 15.00 O 3156 8.00 N 2814 7.00 C 10638 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 836.7 milliseconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 57.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.855A pdb=" N THR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.765A pdb=" N TYR A 50 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 51 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 74 through 88 removed outlier: 4.018A pdb=" N GLU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.547A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.518A pdb=" N VAL A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.000A pdb=" N ALA A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 333 removed outlier: 3.516A pdb=" N ALA A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.538A pdb=" N ARG A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 41 removed outlier: 3.865A pdb=" N THR B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.881A pdb=" N TYR B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 72 through 88 removed outlier: 4.563A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.655A pdb=" N LEU B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.620A pdb=" N ALA B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.641A pdb=" N LEU B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 258 through 284 removed outlier: 3.674A pdb=" N SER B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.695A pdb=" N GLU B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 333 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.587A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 41 removed outlier: 3.529A pdb=" N THR C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.655A pdb=" N TYR C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 Processing helix chain 'C' and resid 72 through 88 removed outlier: 4.227A pdb=" N THR C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 108 through 121 removed outlier: 4.289A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.621A pdb=" N LEU C 129 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.563A pdb=" N ILE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.808A pdb=" N GLU C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 Processing helix chain 'C' and resid 333 through 340 removed outlier: 4.206A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 41 removed outlier: 3.919A pdb=" N THR D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.830A pdb=" N TYR D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 70 Processing helix chain 'D' and resid 72 through 88 removed outlier: 3.597A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.656A pdb=" N ASN D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 108 through 120 removed outlier: 4.204A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.637A pdb=" N LEU D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 211 removed outlier: 3.618A pdb=" N VAL D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.608A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.592A pdb=" N GLU D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 333 Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.500A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.643A pdb=" N THR E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.962A pdb=" N TYR E 50 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.618A pdb=" N GLY E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 removed outlier: 4.374A pdb=" N THR E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 108 through 121 removed outlier: 4.235A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.575A pdb=" N LEU E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.735A pdb=" N ALA E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.604A pdb=" N LEU E 195 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 196 " --> pdb=" O GLY E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 196' Processing helix chain 'E' and resid 200 through 211 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 258 through 284 removed outlier: 3.530A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 288 removed outlier: 5.686A pdb=" N LYS E 288 " --> pdb=" O LYS E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 285 through 288' Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.724A pdb=" N GLU E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 333 Processing helix chain 'E' and resid 333 through 340 removed outlier: 3.587A pdb=" N ARG E 337 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.560A pdb=" N THR F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.689A pdb=" N PHE F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 70 removed outlier: 3.545A pdb=" N GLY F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 88 removed outlier: 3.527A pdb=" N ILE F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 108 through 120 removed outlier: 4.115A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 163 through 172 removed outlier: 3.524A pdb=" N ALA F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.524A pdb=" N ASN F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 removed outlier: 3.636A pdb=" N ILE F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 258 through 284 removed outlier: 3.520A pdb=" N SER F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 311 through 333 Processing helix chain 'F' and resid 333 through 340 removed outlier: 3.566A pdb=" N ARG F 337 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.671A pdb=" N VAL A 138 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 188 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.679A pdb=" N THR A 136 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 11 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR A 55 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 13 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 10 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 227 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 12 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 229 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 14 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 291 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL A 226 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A 293 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 228 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.785A pdb=" N VAL B 138 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 188 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.545A pdb=" N THR B 136 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS B 11 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR B 55 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU B 13 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 57 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 15 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 10 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 227 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 12 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 229 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 14 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 291 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B 226 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE B 293 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 228 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 145 through 149 removed outlier: 3.643A pdb=" N VAL C 138 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 188 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 145 through 149 removed outlier: 3.500A pdb=" N THR C 136 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 11 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR C 55 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU C 13 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 10 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU C 227 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 12 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 229 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER C 14 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 291 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL C 226 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE C 293 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN C 228 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.658A pdb=" N LYS D 11 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR D 55 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU D 13 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 10 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU D 227 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE D 12 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 229 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 14 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL D 291 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 226 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE D 293 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN D 228 " --> pdb=" O ILE D 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.705A pdb=" N ASN D 188 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.723A pdb=" N VAL E 138 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN E 188 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.560A pdb=" N THR E 136 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS E 11 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR E 55 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 13 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 10 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 227 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE E 12 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE E 229 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER E 14 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 291 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL E 226 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE E 293 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN E 228 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.793A pdb=" N VAL F 138 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN F 188 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.564A pdb=" N THR F 136 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS F 11 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR F 55 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU F 13 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE F 10 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU F 227 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE F 12 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE F 229 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER F 14 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL F 291 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL F 226 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE F 293 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN F 228 " --> pdb=" O ILE F 293 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5361 1.35 - 1.46: 3793 1.46 - 1.58: 7730 1.58 - 1.70: 24 1.70 - 1.82: 126 Bond restraints: 17034 Sorted by residual: bond pdb=" CB GLU B 184 " pdb=" CG GLU B 184 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB GLU B 300 " pdb=" CG GLU B 300 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB GLU D 312 " pdb=" CG GLU D 312 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CA THR D 231 " pdb=" C THR D 231 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.47e-02 4.63e+03 9.43e-01 bond pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.81e-01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 22803 2.16 - 4.32: 181 4.32 - 6.48: 22 6.48 - 8.64: 8 8.64 - 10.80: 2 Bond angle restraints: 23016 Sorted by residual: angle pdb=" CB MET F 155 " pdb=" CG MET F 155 " pdb=" SD MET F 155 " ideal model delta sigma weight residual 112.70 123.50 -10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " pdb=" CG GLU B 184 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET D 134 " pdb=" CG MET D 134 " pdb=" SD MET D 134 " ideal model delta sigma weight residual 112.70 103.02 9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N THR D 231 " pdb=" CA THR D 231 " pdb=" C THR D 231 " ideal model delta sigma weight residual 111.71 107.53 4.18 1.34e+00 5.57e-01 9.73e+00 angle pdb=" CA GLN A 97 " pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 ... (remaining 23011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 10175 35.54 - 71.08: 386 71.08 - 106.62: 26 106.62 - 142.16: 1 142.16 - 177.70: 38 Dihedral angle restraints: 10626 sinusoidal: 4632 harmonic: 5994 Sorted by residual: dihedral pdb=" CA LEU B 254 " pdb=" C LEU B 254 " pdb=" N TRP B 255 " pdb=" CA TRP B 255 " ideal model delta harmonic sigma weight residual 180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CAN 4BW A 402 " pdb=" OAV 4BW A 402 " pdb=" PBR 4BW A 402 " pdb=" OAH 4BW A 402 " ideal model delta sinusoidal sigma weight residual -29.82 147.88 -177.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAN 4BW C 401 " pdb=" OAV 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sinusoidal sigma weight residual 330.18 153.03 177.15 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1611 0.029 - 0.058: 629 0.058 - 0.087: 176 0.087 - 0.115: 126 0.115 - 0.144: 20 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA ILE F 297 " pdb=" N ILE F 297 " pdb=" C ILE F 297 " pdb=" CB ILE F 297 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA TYR D 251 " pdb=" N TYR D 251 " pdb=" C TYR D 251 " pdb=" CB TYR D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE D 135 " pdb=" N ILE D 135 " pdb=" C ILE D 135 " pdb=" CB ILE D 135 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2559 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 184 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" CD GLU B 184 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU B 184 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 184 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.012 2.00e-02 2.50e+03 9.83e-03 2.41e+00 pdb=" CG TRP A 99 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 297 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO F 298 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.021 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 715 2.72 - 3.26: 16802 3.26 - 3.81: 27561 3.81 - 4.35: 37161 4.35 - 4.90: 61716 Nonbonded interactions: 143955 Sorted by model distance: nonbonded pdb=" O ILE C 261 " pdb=" OG1 THR C 265 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR E 107 " pdb=" OD2 ASP E 308 " model vdw 2.189 3.040 nonbonded pdb=" N GLU D 312 " pdb=" OE1 GLU D 312 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR D 107 " pdb=" OD2 ASP D 308 " model vdw 2.206 3.040 nonbonded pdb=" N GLN C 97 " pdb=" OE1 GLN C 97 " model vdw 2.223 3.120 ... (remaining 143950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 351) selection = chain 'B' selection = (chain 'C' and resid 8 through 351) selection = (chain 'D' and resid 8 through 351) selection = (chain 'E' and resid 8 through 351) selection = (chain 'F' and resid 8 through 351) } 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: 1.470 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.090 Find NCS groups from input model: 0.460 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.002 0.041 17035 Z= 0.081 Angle : 0.482 10.804 23016 Z= 0.237 Chirality : 0.039 0.144 2562 Planarity : 0.003 0.049 2892 Dihedral : 21.007 177.703 6762 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 1.85 % Allowed : 27.44 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.19), residues: 2052 helix: 0.60 (0.17), residues: 990 sheet: 0.53 (0.33), residues: 264 loop : -0.40 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 279 TYR 0.006 0.001 TYR B 107 PHE 0.013 0.001 PHE F 156 TRP 0.026 0.003 TRP A 99 HIS 0.002 0.001 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (17034) covalent geometry : angle 0.48184 / 0.24 (23016) hydrogen bonds : bond 0.23532 / 15.92 ( 744) hydrogen bonds : angle 7.52366 / 5.23 ( 2217) Misc. bond : bond 0.00235 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.687 Fit side-chains REVERT: A 134 MET cc_start: 0.9162 (ttp) cc_final: 0.8946 (ttp) REVERT: B 158 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7442 (tmm) REVERT: C 295 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: D 222 GLU cc_start: 0.8769 (tt0) cc_final: 0.8293 (tm-30) REVERT: D 295 GLU cc_start: 0.8829 (pt0) cc_final: 0.8132 (pp20) REVERT: D 325 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9105 (mp) REVERT: E 97 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: E 137 SER cc_start: 0.9371 (t) cc_final: 0.9015 (p) REVERT: E 155 MET cc_start: 0.9202 (mmp) cc_final: 0.8081 (tmt) REVERT: F 97 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: F 251 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7475 (m-80) outliers start: 33 outliers final: 20 residues processed: 136 average time/residue: 0.5635 time to fit residues: 87.1645 Evaluate side-chains 130 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.8291 > 50:) chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN E 271 HIS E 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063481 restraints weight = 32932.485| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.80 r_work: 0.2847 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17035 Z= 0.150 Angle : 0.533 7.972 23016 Z= 0.276 Chirality : 0.042 0.156 2562 Planarity : 0.004 0.053 2892 Dihedral : 22.426 178.992 2657 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 4.10 % Allowed : 22.90 % Favored : 73.01 % 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: 0.53 (0.19), residues: 2052 helix: 0.90 (0.16), residues: 1038 sheet: 0.50 (0.32), residues: 264 loop : -0.33 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 279 TYR 0.009 0.001 TYR F 330 PHE 0.020 0.001 PHE F 156 TRP 0.022 0.002 TRP B 255 HIS 0.003 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (17034) covalent geometry : angle 0.53309 / 0.28 (23016) hydrogen bonds : bond 0.04603 / 3.02 ( 744) hydrogen bonds : angle 5.19937 / 3.66 ( 2217) Misc. bond : bond 0.00289 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 117 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.9043 (mtp) cc_final: 0.8833 (mtp) REVERT: B 158 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: C 21 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8638 (mpt-90) REVERT: D 86 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8527 (mmtp) REVERT: D 220 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7547 (ptpp) REVERT: D 222 GLU cc_start: 0.8804 (tt0) cc_final: 0.8337 (tm-30) REVERT: D 255 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.6695 (m100) REVERT: D 295 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: D 300 GLU cc_start: 0.7789 (mp0) cc_final: 0.7453 (pm20) REVERT: E 158 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.6769 (tmt) REVERT: F 97 GLN cc_start: 0.7909 (mm110) cc_final: 0.7259 (mp10) REVERT: F 251 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7506 (m-80) outliers start: 73 outliers final: 23 residues processed: 176 average time/residue: 0.5264 time to fit residues: 105.7742 Evaluate side-chains 134 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062248 restraints weight = 33695.283| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.80 r_work: 0.2818 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17035 Z= 0.192 Angle : 0.546 10.223 23016 Z= 0.279 Chirality : 0.043 0.162 2562 Planarity : 0.004 0.057 2892 Dihedral : 22.395 179.383 2624 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 4.71 % Allowed : 21.60 % Favored : 73.68 % 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: 0.50 (0.19), residues: 2052 helix: 0.94 (0.16), residues: 1038 sheet: 0.37 (0.32), residues: 264 loop : -0.41 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 279 TYR 0.010 0.001 TYR D 251 PHE 0.023 0.001 PHE F 156 TRP 0.021 0.003 TRP B 255 HIS 0.004 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (17034) covalent geometry : angle 0.54613 / 0.28 (23016) hydrogen bonds : bond 0.04338 / 2.86 ( 744) hydrogen bonds : angle 4.95541 / 3.49 ( 2217) Misc. bond : bond 0.00306 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 107 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7410 (tmm) REVERT: C 21 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8657 (mpt-90) REVERT: C 108 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: C 158 MET cc_start: 0.8469 (tpp) cc_final: 0.8205 (tpp) REVERT: D 86 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8571 (mmtp) REVERT: D 222 GLU cc_start: 0.8835 (tt0) cc_final: 0.8386 (tm-30) REVERT: D 238 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 255 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.6834 (m100) REVERT: D 300 GLU cc_start: 0.7675 (mp0) cc_final: 0.7308 (pm20) REVERT: E 158 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.6492 (tmt) REVERT: F 42 CYS cc_start: 0.8348 (t) cc_final: 0.7425 (m) REVERT: F 97 GLN cc_start: 0.7940 (mm110) cc_final: 0.7299 (mp10) REVERT: F 152 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8085 (p-80) REVERT: F 251 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7538 (m-80) outliers start: 84 outliers final: 41 residues processed: 177 average time/residue: 0.4581 time to fit residues: 94.1199 Evaluate side-chains 152 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 331 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 0.5980 chunk 58 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063658 restraints weight = 33301.824| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.79 r_work: 0.2845 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17035 Z= 0.134 Angle : 0.512 10.127 23016 Z= 0.260 Chirality : 0.041 0.155 2562 Planarity : 0.004 0.053 2892 Dihedral : 22.311 179.865 2622 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 3.87 % Allowed : 22.56 % Favored : 73.57 % 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: 0.59 (0.19), residues: 2052 helix: 1.05 (0.17), residues: 1038 sheet: 0.34 (0.32), residues: 264 loop : -0.40 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 279 TYR 0.007 0.001 TYR D 251 PHE 0.019 0.001 PHE F 156 TRP 0.022 0.003 TRP B 255 HIS 0.002 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17034) covalent geometry : angle 0.51245 / 0.26 (23016) hydrogen bonds : bond 0.03753 / 2.47 ( 744) hydrogen bonds : angle 4.74508 / 3.34 ( 2217) Misc. bond : bond 0.00282 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 103 time to evaluate : 0.706 Fit side-chains REVERT: B 158 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: C 152 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8825 (p-80) REVERT: C 158 MET cc_start: 0.8452 (tpp) cc_final: 0.8134 (tpp) REVERT: C 295 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: D 86 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8550 (mmtp) REVERT: D 222 GLU cc_start: 0.8810 (tt0) cc_final: 0.8352 (tm-30) REVERT: D 238 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8642 (mm) REVERT: D 255 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.6749 (m100) REVERT: D 295 GLU cc_start: 0.8918 (pt0) cc_final: 0.8268 (pp20) REVERT: D 300 GLU cc_start: 0.7596 (mp0) cc_final: 0.7252 (pm20) REVERT: E 97 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 99 TRP cc_start: 0.8017 (p90) cc_final: 0.7776 (p90) REVERT: E 280 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8652 (tp30) REVERT: F 42 CYS cc_start: 0.8321 (t) cc_final: 0.7448 (m) REVERT: F 97 GLN cc_start: 0.7936 (mm110) cc_final: 0.7219 (mp10) REVERT: F 152 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8068 (p-80) REVERT: F 251 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7521 (m-80) outliers start: 69 outliers final: 36 residues processed: 160 average time/residue: 0.5004 time to fit residues: 91.9955 Evaluate side-chains 145 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN B 97 GLN B 228 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064050 restraints weight = 33008.372| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.78 r_work: 0.2861 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17035 Z= 0.120 Angle : 0.507 10.451 23016 Z= 0.255 Chirality : 0.041 0.153 2562 Planarity : 0.003 0.039 2892 Dihedral : 22.258 179.624 2622 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 4.38 % Allowed : 22.11 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.19), residues: 2052 helix: 1.11 (0.17), residues: 1038 sheet: 0.32 (0.32), residues: 264 loop : -0.38 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 279 TYR 0.007 0.001 TYR D 251 PHE 0.020 0.001 PHE F 156 TRP 0.022 0.003 TRP B 255 HIS 0.002 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17034) covalent geometry : angle 0.50656 / 0.25 (23016) hydrogen bonds : bond 0.03564 / 2.34 ( 744) hydrogen bonds : angle 4.64153 / 3.27 ( 2217) Misc. bond : bond 0.00244 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 106 time to evaluate : 0.658 Fit side-chains REVERT: A 97 GLN cc_start: 0.8278 (mp10) cc_final: 0.8030 (mp-120) REVERT: B 97 GLN cc_start: 0.7214 (pt0) cc_final: 0.7001 (pt0) REVERT: C 152 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8841 (p-80) REVERT: C 295 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: C 307 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8410 (tp) REVERT: D 86 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8560 (mmtp) REVERT: D 222 GLU cc_start: 0.8806 (tt0) cc_final: 0.8341 (tm-30) REVERT: D 255 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.6709 (m100) REVERT: D 295 GLU cc_start: 0.8925 (pt0) cc_final: 0.8337 (pp20) REVERT: D 300 GLU cc_start: 0.7551 (mp0) cc_final: 0.7209 (pm20) REVERT: D 325 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9097 (mm) REVERT: E 97 GLN cc_start: 0.7872 (tm-30) cc_final: 0.6992 (tm-30) REVERT: E 99 TRP cc_start: 0.8077 (p90) cc_final: 0.7763 (p90) REVERT: F 42 CYS cc_start: 0.8272 (t) cc_final: 0.7385 (m) REVERT: F 97 GLN cc_start: 0.7915 (mm110) cc_final: 0.7251 (mp10) REVERT: F 152 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8067 (p-80) REVERT: F 251 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7466 (m-80) outliers start: 78 outliers final: 46 residues processed: 173 average time/residue: 0.4766 time to fit residues: 95.3142 Evaluate side-chains 158 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 104 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 203 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066415 restraints weight = 32659.197| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.78 r_work: 0.2910 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17035 Z= 0.087 Angle : 0.486 9.149 23016 Z= 0.240 Chirality : 0.040 0.159 2562 Planarity : 0.003 0.032 2892 Dihedral : 22.062 179.982 2619 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 3.14 % Allowed : 23.29 % Favored : 73.57 % 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: 0.77 (0.19), residues: 2052 helix: 1.27 (0.17), residues: 1032 sheet: 0.37 (0.32), residues: 264 loop : -0.40 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 279 TYR 0.006 0.001 TYR C 330 PHE 0.014 0.001 PHE F 156 TRP 0.024 0.003 TRP B 255 HIS 0.001 0.000 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 (17034) covalent geometry : angle 0.48621 / 0.24 (23016) hydrogen bonds : bond 0.03145 / 2.06 ( 744) hydrogen bonds : angle 4.48788 / 3.16 ( 2217) Misc. bond : bond 0.00182 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 0.510 Fit side-chains REVERT: C 158 MET cc_start: 0.8251 (tpp) cc_final: 0.7997 (tpp) REVERT: C 295 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: D 222 GLU cc_start: 0.8801 (tt0) cc_final: 0.8317 (tm-30) REVERT: D 295 GLU cc_start: 0.8968 (pt0) cc_final: 0.8299 (pp20) REVERT: D 300 GLU cc_start: 0.7498 (mp0) cc_final: 0.7185 (pm20) REVERT: D 325 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9092 (mm) REVERT: E 97 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: E 99 TRP cc_start: 0.8120 (p90) cc_final: 0.7736 (p90) REVERT: E 155 MET cc_start: 0.9120 (mmp) cc_final: 0.7994 (tmt) REVERT: E 295 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: F 42 CYS cc_start: 0.8258 (t) cc_final: 0.7367 (m) REVERT: F 97 GLN cc_start: 0.7846 (mm110) cc_final: 0.7098 (mp10) REVERT: F 251 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7378 (m-80) outliers start: 56 outliers final: 29 residues processed: 168 average time/residue: 0.4411 time to fit residues: 84.7498 Evaluate side-chains 143 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.0040 chunk 172 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 ASN B 299 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.066057 restraints weight = 32516.697| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.77 r_work: 0.2904 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17035 Z= 0.100 Angle : 0.506 9.319 23016 Z= 0.251 Chirality : 0.040 0.144 2562 Planarity : 0.003 0.034 2892 Dihedral : 22.077 179.274 2619 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.09 % Allowed : 23.96 % Favored : 72.95 % 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: 0.75 (0.19), residues: 2052 helix: 1.16 (0.17), residues: 1056 sheet: 0.40 (0.32), residues: 264 loop : -0.31 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 279 TYR 0.006 0.001 TYR D 251 PHE 0.018 0.001 PHE F 156 TRP 0.028 0.003 TRP A 99 HIS 0.003 0.001 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (17034) covalent geometry : angle 0.50630 / 0.25 (23016) hydrogen bonds : bond 0.03193 / 2.10 ( 744) hydrogen bonds : angle 4.46873 / 3.15 ( 2217) Misc. bond : bond 0.00183 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 0.499 Fit side-chains REVERT: B 158 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7220 (tmm) REVERT: C 152 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8663 (p-80) REVERT: C 295 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: D 222 GLU cc_start: 0.8808 (tt0) cc_final: 0.8322 (tm-30) REVERT: D 295 GLU cc_start: 0.8947 (pt0) cc_final: 0.8280 (pp20) REVERT: D 300 GLU cc_start: 0.7500 (mp0) cc_final: 0.7093 (pm20) REVERT: D 325 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9101 (mm) REVERT: E 97 GLN cc_start: 0.7825 (tm-30) cc_final: 0.6861 (tm-30) REVERT: E 99 TRP cc_start: 0.8100 (p90) cc_final: 0.7664 (p90) REVERT: E 155 MET cc_start: 0.9049 (mmp) cc_final: 0.8010 (tmt) REVERT: E 295 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: F 97 GLN cc_start: 0.7855 (mm110) cc_final: 0.7106 (mp10) REVERT: F 251 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7316 (m-80) outliers start: 55 outliers final: 35 residues processed: 153 average time/residue: 0.4258 time to fit residues: 74.7719 Evaluate side-chains 143 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 65 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 22 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064433 restraints weight = 33051.553| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.80 r_work: 0.2877 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17035 Z= 0.134 Angle : 0.525 9.637 23016 Z= 0.261 Chirality : 0.041 0.190 2562 Planarity : 0.003 0.039 2892 Dihedral : 22.121 177.977 2617 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.31 % Allowed : 23.85 % Favored : 72.84 % 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: 0.73 (0.19), residues: 2052 helix: 1.14 (0.17), residues: 1056 sheet: 0.40 (0.32), residues: 264 loop : -0.33 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 279 TYR 0.008 0.001 TYR D 251 PHE 0.021 0.001 PHE F 156 TRP 0.055 0.003 TRP B 99 HIS 0.003 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (17034) covalent geometry : angle 0.52526 / 0.26 (23016) hydrogen bonds : bond 0.03401 / 2.24 ( 744) hydrogen bonds : angle 4.50397 / 3.17 ( 2217) Misc. bond : bond 0.00218 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 104 time to evaluate : 0.512 Fit side-chains REVERT: B 158 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: C 158 MET cc_start: 0.8366 (tpp) cc_final: 0.8083 (tpp) REVERT: C 295 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: D 222 GLU cc_start: 0.8806 (tt0) cc_final: 0.8395 (tm-30) REVERT: D 295 GLU cc_start: 0.8966 (pt0) cc_final: 0.8287 (pp20) REVERT: D 300 GLU cc_start: 0.7534 (mp0) cc_final: 0.7210 (pm20) REVERT: D 325 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9114 (mm) REVERT: E 97 GLN cc_start: 0.7795 (tm-30) cc_final: 0.6897 (tm-30) REVERT: E 99 TRP cc_start: 0.8135 (p90) cc_final: 0.7684 (p90) REVERT: E 280 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8664 (tp30) REVERT: F 97 GLN cc_start: 0.7936 (mm110) cc_final: 0.7179 (mp10) REVERT: F 251 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7413 (m-80) outliers start: 59 outliers final: 37 residues processed: 155 average time/residue: 0.3755 time to fit residues: 67.4186 Evaluate side-chains 145 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 148 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.062596 restraints weight = 33365.951| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.78 r_work: 0.2826 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17035 Z= 0.202 Angle : 0.577 10.317 23016 Z= 0.287 Chirality : 0.043 0.181 2562 Planarity : 0.004 0.049 2892 Dihedral : 22.337 176.697 2617 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.20 % Allowed : 24.07 % Favored : 72.73 % 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: 0.62 (0.19), residues: 2052 helix: 1.05 (0.17), residues: 1056 sheet: 0.34 (0.32), residues: 264 loop : -0.37 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 279 TYR 0.010 0.001 TYR D 251 PHE 0.028 0.001 PHE F 156 TRP 0.049 0.003 TRP B 99 HIS 0.004 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (17034) covalent geometry : angle 0.57714 / 0.29 (23016) hydrogen bonds : bond 0.03849 / 2.54 ( 744) hydrogen bonds : angle 4.64364 / 3.27 ( 2217) Misc. bond : bond 0.00289 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 0.713 Fit side-chains REVERT: B 158 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7311 (tmm) REVERT: D 222 GLU cc_start: 0.8828 (tt0) cc_final: 0.8396 (tm-30) REVERT: D 238 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8684 (mm) REVERT: D 257 MET cc_start: 0.8124 (mmm) cc_final: 0.7836 (mmm) REVERT: D 295 GLU cc_start: 0.8924 (pt0) cc_final: 0.8209 (pp20) REVERT: D 300 GLU cc_start: 0.7490 (mp0) cc_final: 0.7235 (pm20) REVERT: D 325 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9179 (mm) REVERT: E 97 GLN cc_start: 0.7760 (tm-30) cc_final: 0.6751 (tm-30) REVERT: E 99 TRP cc_start: 0.8191 (p90) cc_final: 0.7640 (p90) REVERT: E 155 MET cc_start: 0.9180 (mmp) cc_final: 0.8017 (tmt) REVERT: E 280 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8693 (tp30) REVERT: F 97 GLN cc_start: 0.7982 (mm110) cc_final: 0.7215 (mp10) REVERT: F 187 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: F 251 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7481 (m-80) outliers start: 57 outliers final: 40 residues processed: 152 average time/residue: 0.4839 time to fit residues: 84.9576 Evaluate side-chains 150 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 188 ASN B 228 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064935 restraints weight = 32860.608| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.78 r_work: 0.2878 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17035 Z= 0.107 Angle : 0.533 11.008 23016 Z= 0.263 Chirality : 0.041 0.179 2562 Planarity : 0.003 0.034 2892 Dihedral : 22.153 178.282 2617 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.36 % Allowed : 25.08 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.19), residues: 2052 helix: 1.18 (0.17), residues: 1044 sheet: 0.32 (0.32), residues: 264 loop : -0.38 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 279 TYR 0.006 0.001 TYR D 251 PHE 0.019 0.001 PHE F 156 TRP 0.041 0.003 TRP B 99 HIS 0.002 0.001 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (17034) covalent geometry : angle 0.53317 / 0.26 (23016) hydrogen bonds : bond 0.03347 / 2.20 ( 744) hydrogen bonds : angle 4.53585 / 3.19 ( 2217) Misc. bond : bond 0.00227 / 0.12 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8987 (mtp) cc_final: 0.8763 (mtp) REVERT: B 158 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7359 (tmm) REVERT: C 158 MET cc_start: 0.8328 (tpp) cc_final: 0.8018 (tpp) REVERT: D 222 GLU cc_start: 0.8822 (tt0) cc_final: 0.8341 (tm-30) REVERT: D 257 MET cc_start: 0.8160 (mmm) cc_final: 0.7864 (mmm) REVERT: D 295 GLU cc_start: 0.8927 (pt0) cc_final: 0.8224 (pp20) REVERT: D 300 GLU cc_start: 0.7408 (mp0) cc_final: 0.7137 (pm20) REVERT: E 97 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7243 (tm-30) REVERT: E 155 MET cc_start: 0.9104 (mmp) cc_final: 0.7993 (tmt) REVERT: F 97 GLN cc_start: 0.7895 (mm110) cc_final: 0.7143 (mp10) REVERT: F 251 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7401 (m-80) outliers start: 42 outliers final: 32 residues processed: 144 average time/residue: 0.4797 time to fit residues: 79.4924 Evaluate side-chains 135 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 169 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065841 restraints weight = 32838.766| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.79 r_work: 0.2901 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17035 Z= 0.100 Angle : 0.535 11.223 23016 Z= 0.262 Chirality : 0.041 0.196 2562 Planarity : 0.003 0.035 2892 Dihedral : 22.060 179.790 2617 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.02 % Allowed : 25.42 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.19), residues: 2052 helix: 1.18 (0.17), residues: 1050 sheet: 0.35 (0.32), residues: 264 loop : -0.35 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 279 TYR 0.007 0.001 TYR D 251 PHE 0.018 0.001 PHE F 156 TRP 0.072 0.004 TRP B 99 HIS 0.002 0.000 HIS F 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (17034) covalent geometry : angle 0.53465 / 0.26 (23016) hydrogen bonds : bond 0.03208 / 2.11 ( 744) hydrogen bonds : angle 4.44956 / 3.13 ( 2217) Misc. bond : bond 0.00208 / 0.11 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.47 seconds wall clock time: 78 minutes 0.40 seconds (4680.40 seconds total)