Starting phenix.real_space_refine on Thu Mar 5 05:17:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbo_64929/03_2026/9vbo_64929.map" } resolution = 2.16 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= 0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 82 5.16 5 C 12183 2.51 5 N 3186 2.21 5 O 3714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19167 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2777 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 346} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2718 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 8, 'TRANS': 338} Chain: "C" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2718 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 8, 'TRANS': 338} Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2780 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 346} Chain: "H" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1169 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2915 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2915 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 140} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11253 SG CYS H 33 59.628 76.351 31.074 1.00 40.43 S ATOM 11276 SG CYS H 36 62.578 78.434 31.513 1.00 45.71 S ATOM 11377 SG CYS H 47 60.574 77.438 34.554 1.00 35.96 S ATOM 11402 SG CYS H 50 58.853 79.760 31.931 1.00 39.57 S ATOM 18252 SG CYS G 33 42.774 76.554 92.727 1.00 42.74 S ATOM 18275 SG CYS G 36 40.036 79.009 92.324 1.00 47.69 S ATOM 18376 SG CYS G 47 41.884 77.788 89.228 1.00 36.73 S ATOM 18401 SG CYS G 50 43.682 80.004 91.877 1.00 41.33 S Time building chain proxies: 3.99, per 1000 atoms: 0.21 Number of scatterers: 19167 At special positions: 0 Unit cell: (103.824, 109.386, 125.145, 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) Zn 2 29.99 S 82 16.00 O 3714 8.00 N 3186 7.00 C 12183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 801.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 36 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 50 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 47 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 33 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 47 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 36 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 50 " Number of angles added : 12 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 18 sheets defined 41.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.956A pdb=" N GLN A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.893A pdb=" N ILE A 161 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 278 through 292 removed outlier: 4.588A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.524A pdb=" N VAL B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.786A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.625A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.546A pdb=" N ASP B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.693A pdb=" N GLN C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.922A pdb=" N ILE C 161 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 216 through 232 Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 278 through 290 removed outlier: 4.624A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.953A pdb=" N ASP C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'D' and resid 22 through 30 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.794A pdb=" N GLN D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.913A pdb=" N ILE D 161 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 278 through 292 removed outlier: 4.614A pdb=" N ILE D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 337 through 345 Processing helix chain 'H' and resid 15 through 21 removed outlier: 3.712A pdb=" N GLU H 21 " --> pdb=" O LYS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 27 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 56 through 61 removed outlier: 4.111A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 74 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.630A pdb=" N ILE E 120 " --> pdb=" O MET E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.747A pdb=" N LEU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 143 through 150 removed outlier: 3.807A pdb=" N PHE E 147 " --> pdb=" O HIS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 158 removed outlier: 3.960A pdb=" N SER E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.951A pdb=" N VAL E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 247 through 257 removed outlier: 5.704A pdb=" N GLU E 254 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS E 255 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 256 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 304 through 313 Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 353 through 367 removed outlier: 4.151A pdb=" N TYR E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 56 through 61 removed outlier: 4.111A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 88 through 103 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.619A pdb=" N ILE F 120 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 removed outlier: 3.748A pdb=" N LEU F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 143 through 150 removed outlier: 3.807A pdb=" N PHE F 147 " --> pdb=" O HIS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 158 removed outlier: 3.960A pdb=" N SER F 155 " --> pdb=" O GLN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.951A pdb=" N VAL F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 247 through 257 removed outlier: 5.705A pdb=" N GLU F 254 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS F 255 " --> pdb=" O TYR F 252 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 256 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'F' and resid 342 through 347 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 353 through 367 removed outlier: 4.151A pdb=" N TYR F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 21 removed outlier: 3.703A pdb=" N GLU G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 113 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.453A pdb=" N TYR A 241 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS A 301 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 243 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR A 303 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER A 309 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A 185 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR A 311 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 183 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 313 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 178 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 6 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 169 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR A 11 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 167 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A 13 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 165 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 138 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 79 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP A 78 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N CYS A 111 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 80 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A 113 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 82 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 78 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N CYS B 111 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 80 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE B 113 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 82 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 138 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 79 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 165 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE B 13 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER B 167 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR B 11 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 169 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE B 6 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 178 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 313 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 183 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR B 311 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN B 185 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER B 309 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 241 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N CYS B 301 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 243 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 303 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.245A pdb=" N PHE A 18 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.336A pdb=" N PHE B 18 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 Processing sheet with id=AA6, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.336A pdb=" N TYR C 241 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N CYS C 301 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 243 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR C 303 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER C 309 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN C 185 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR C 311 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C 183 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 313 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 178 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE C 6 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 169 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR C 11 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER C 167 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C 13 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 165 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 138 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 79 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP C 78 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N CYS C 111 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 80 " --> pdb=" O CYS C 111 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE C 113 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 82 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP D 78 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N CYS D 111 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 80 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE D 113 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 82 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR D 138 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 79 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA D 165 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE D 13 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER D 167 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR D 11 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 169 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE D 6 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 178 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE D 313 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE D 183 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR D 311 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN D 185 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 309 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR D 241 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N CYS D 301 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 243 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR D 303 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 48 removed outlier: 4.273A pdb=" N PHE C 18 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 193 through 194 Processing sheet with id=AA9, first strand: chain 'D' and resid 45 through 48 removed outlier: 4.176A pdb=" N PHE D 18 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 193 through 194 Processing sheet with id=AB2, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AB3, first strand: chain 'H' and resid 63 through 72 removed outlier: 6.597A pdb=" N VAL H 92 " --> pdb=" O LYS H 67 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE H 69 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU H 90 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE H 71 " --> pdb=" O ARG H 88 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG H 88 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR H 89 " --> pdb=" O ILE H 105 " (cutoff:3.500A) removed outlier: 18.770A pdb=" N ASP H 100 " --> pdb=" O TYR H 139 " (cutoff:3.500A) removed outlier: 13.334A pdb=" N TYR H 141 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU H 102 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE H 143 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU H 104 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU H 145 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE H 106 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS H 138 " --> pdb=" O GLN H 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 12 removed outlier: 6.449A pdb=" N ILE E 218 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL E 10 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA E 216 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS E 12 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA E 214 " --> pdb=" O CYS E 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 234 through 243 removed outlier: 6.459A pdb=" N VAL E 397 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG E 239 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA E 395 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR E 241 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA E 393 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 296 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 12 removed outlier: 6.450A pdb=" N ILE F 218 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL F 10 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA F 216 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS F 12 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA F 214 " --> pdb=" O CYS F 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 234 through 243 removed outlier: 6.459A pdb=" N VAL F 397 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG F 239 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA F 395 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR F 241 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA F 393 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 296 " --> pdb=" O TYR F 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AB9, first strand: chain 'G' and resid 63 through 72 removed outlier: 5.510A pdb=" N ILE G 66 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU G 94 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR G 89 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 18.784A pdb=" N ASP G 100 " --> pdb=" O TYR G 139 " (cutoff:3.500A) removed outlier: 13.326A pdb=" N TYR G 141 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LEU G 102 " --> pdb=" O TYR G 141 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE G 143 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU G 104 " --> pdb=" O PHE G 143 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU G 145 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS G 138 " --> pdb=" O GLN G 129 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2283 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: 3.84 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3593 1.32 - 1.44: 4775 1.44 - 1.57: 11009 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 19509 Sorted by residual: bond pdb=" SG SCY F 87 " pdb=" CD SCY F 87 " ideal model delta sigma weight residual 1.703 1.766 -0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" SG SCY E 87 " pdb=" CD SCY E 87 " ideal model delta sigma weight residual 1.703 1.766 -0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" N VAL G 126 " pdb=" CA VAL G 126 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.28e+00 bond pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 8.03e+00 bond pdb=" CA ALA B 115 " pdb=" CB ALA B 115 " ideal model delta sigma weight residual 1.529 1.501 0.028 1.02e-02 9.61e+03 7.57e+00 ... (remaining 19504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 25768 2.17 - 4.34: 468 4.34 - 6.51: 57 6.51 - 8.68: 5 8.68 - 10.85: 5 Bond angle restraints: 26303 Sorted by residual: angle pdb=" O SCY F 87 " pdb=" C SCY F 87 " pdb=" N ALA F 88 " ideal model delta sigma weight residual 123.00 112.70 10.30 1.60e+00 3.91e-01 4.14e+01 angle pdb=" O SCY E 87 " pdb=" C SCY E 87 " pdb=" N ALA E 88 " ideal model delta sigma weight residual 123.00 112.73 10.27 1.60e+00 3.91e-01 4.12e+01 angle pdb=" N ASN A 94 " pdb=" CA ASN A 94 " pdb=" C ASN A 94 " ideal model delta sigma weight residual 112.89 107.08 5.81 1.24e+00 6.50e-01 2.20e+01 angle pdb=" N ASN B 106 " pdb=" CA ASN B 106 " pdb=" C ASN B 106 " ideal model delta sigma weight residual 114.56 109.25 5.31 1.27e+00 6.20e-01 1.75e+01 angle pdb=" N ASN B 118 " pdb=" CA ASN B 118 " pdb=" C ASN B 118 " ideal model delta sigma weight residual 112.92 108.06 4.86 1.23e+00 6.61e-01 1.56e+01 ... (remaining 26298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10440 17.76 - 35.52: 944 35.52 - 53.28: 239 53.28 - 71.04: 65 71.04 - 88.80: 25 Dihedral angle restraints: 11713 sinusoidal: 4625 harmonic: 7088 Sorted by residual: dihedral pdb=" CA GLU G 13 " pdb=" C GLU G 13 " pdb=" N SER G 14 " pdb=" CA SER G 14 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY E 64 " pdb=" C GLY E 64 " pdb=" N ILE E 65 " pdb=" CA ILE E 65 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY F 64 " pdb=" C GLY F 64 " pdb=" N ILE F 65 " pdb=" CA ILE F 65 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 11710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2233 0.055 - 0.110: 572 0.110 - 0.165: 112 0.165 - 0.220: 7 0.220 - 0.274: 3 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CA ILE C 113 " pdb=" N ILE C 113 " pdb=" C ILE C 113 " pdb=" CB ILE C 113 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE D 113 " pdb=" N ILE D 113 " pdb=" C ILE D 113 " pdb=" CB ILE D 113 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE A 113 " pdb=" N ILE A 113 " pdb=" C ILE A 113 " pdb=" CB ILE A 113 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2924 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SCY E 87 " 0.068 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C SCY E 87 " -0.225 2.00e-02 2.50e+03 pdb=" O SCY E 87 " 0.081 2.00e-02 2.50e+03 pdb=" N ALA E 88 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SCY F 87 " -0.068 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C SCY F 87 " 0.225 2.00e-02 2.50e+03 pdb=" O SCY F 87 " -0.081 2.00e-02 2.50e+03 pdb=" N ALA F 88 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 114 " -0.350 9.50e-02 1.11e+02 1.57e-01 1.51e+01 pdb=" NE ARG A 114 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 114 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 114 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 114 " -0.013 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1601 2.74 - 3.28: 19257 3.28 - 3.82: 35051 3.82 - 4.36: 44978 4.36 - 4.90: 73124 Nonbonded interactions: 174011 Sorted by model distance: nonbonded pdb=" OE2 GLU D 192 " pdb=" OH TYR D 303 " model vdw 2.200 3.040 nonbonded pdb=" O PRO A 16 " pdb=" NH1 ARG A 19 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR F 153 " pdb=" OE2 GLU F 311 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR E 153 " pdb=" OE2 GLU E 311 " model vdw 2.216 3.040 nonbonded pdb=" O PRO B 16 " pdb=" NH1 ARG B 19 " model vdw 2.224 3.120 ... (remaining 174006 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 5 through 351) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 5 through 351) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 109 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or resid 111 through 201)) selection = chain 'H' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.200 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.006 0.066 19517 Z= 0.274 Angle : 0.723 10.851 26315 Z= 0.433 Chirality : 0.051 0.274 2927 Planarity : 0.007 0.157 3393 Dihedral : 15.628 88.796 7193 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.29 % Allowed : 12.06 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.14 (0.17), residues: 2436 helix: 0.35 (0.17), residues: 866 sheet: 0.15 (0.24), residues: 476 loop : 0.04 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 107 TYR 0.019 0.002 TYR F 34 PHE 0.027 0.002 PHE H 2 TRP 0.015 0.003 TRP C 29 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00551 (19509) covalent geometry : angle 0.71733 (26303) hydrogen bonds : bond 0.13780 ( 841) hydrogen bonds : angle 6.45436 ( 2283) metal coordination : bond 0.01377 ( 8) metal coordination : angle 4.46877 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 235 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7306 (mmmt) REVERT: E 129 MET cc_start: 0.7988 (mtp) cc_final: 0.7773 (mtp) REVERT: E 175 MET cc_start: 0.8463 (mmp) cc_final: 0.8030 (mmp) REVERT: F 100 MET cc_start: 0.8610 (mtp) cc_final: 0.8297 (mtp) REVERT: F 124 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7167 (pm20) REVERT: F 201 GLN cc_start: 0.7602 (mt0) cc_final: 0.7357 (mt0) outliers start: 6 outliers final: 3 residues processed: 234 average time/residue: 0.6960 time to fit residues: 180.0932 Evaluate side-chains 206 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN B 332 ASN D 332 ASN H 9 ASN H 35 HIS E 201 GLN E 282 GLN E 327 ASN E 349 HIS F 327 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104890 restraints weight = 18422.548| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.20 r_work: 0.3106 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19517 Z= 0.153 Angle : 0.556 7.340 26315 Z= 0.304 Chirality : 0.046 0.165 2927 Planarity : 0.004 0.042 3393 Dihedral : 5.330 58.756 2657 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.58 % Allowed : 11.00 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.44 (0.17), residues: 2436 helix: 0.70 (0.17), residues: 882 sheet: 0.17 (0.23), residues: 522 loop : 0.20 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 107 TYR 0.016 0.002 TYR E 153 PHE 0.027 0.002 PHE H 2 TRP 0.012 0.002 TRP A 29 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00332 (19509) covalent geometry : angle 0.54991 (26303) hydrogen bonds : bond 0.04793 ( 841) hydrogen bonds : angle 5.30138 ( 2283) metal coordination : bond 0.01136 ( 8) metal coordination : angle 3.96281 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 GLN cc_start: 0.8073 (mt0) cc_final: 0.7857 (mt0) REVERT: C 155 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: D 33 ASN cc_start: 0.8617 (t0) cc_final: 0.8230 (t0) REVERT: D 155 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 200 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.7812 (ttt180) REVERT: D 285 MET cc_start: 0.9030 (tmm) cc_final: 0.8630 (tmm) REVERT: H 94 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: E 124 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7953 (tp30) REVERT: E 175 MET cc_start: 0.8719 (mmp) cc_final: 0.8304 (mmp) REVERT: E 222 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7172 (ptm) REVERT: E 282 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.6332 (tm130) outliers start: 33 outliers final: 11 residues processed: 239 average time/residue: 0.7344 time to fit residues: 194.4347 Evaluate side-chains 227 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 95 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN B 332 ASN C 69 HIS D 199 ASN D 332 ASN H 9 ASN H 35 HIS E 258 HIS E 327 ASN F 327 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105315 restraints weight = 18689.042| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.23 r_work: 0.3113 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19517 Z= 0.147 Angle : 0.536 7.201 26315 Z= 0.293 Chirality : 0.045 0.156 2927 Planarity : 0.004 0.041 3393 Dihedral : 5.223 59.576 2657 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.48 % Allowed : 11.39 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.47 (0.17), residues: 2436 helix: 0.75 (0.17), residues: 884 sheet: 0.16 (0.23), residues: 528 loop : 0.21 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 107 TYR 0.017 0.002 TYR F 34 PHE 0.025 0.002 PHE H 2 TRP 0.012 0.002 TRP A 29 HIS 0.005 0.001 HIS E 349 Details of bonding type rmsd covalent geometry : bond 0.00320 (19509) covalent geometry : angle 0.52983 (26303) hydrogen bonds : bond 0.04528 ( 841) hydrogen bonds : angle 5.17399 ( 2283) metal coordination : bond 0.01072 ( 8) metal coordination : angle 3.68912 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6804 (mt-10) REVERT: C 155 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: D 33 ASN cc_start: 0.8573 (t0) cc_final: 0.8148 (t0) REVERT: D 155 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: D 285 MET cc_start: 0.9042 (tmm) cc_final: 0.8694 (tmm) REVERT: H 94 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: E 124 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7935 (tp30) REVERT: E 175 MET cc_start: 0.8669 (mmp) cc_final: 0.8257 (mmp) REVERT: F 124 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7207 (pt0) outliers start: 31 outliers final: 13 residues processed: 234 average time/residue: 0.6914 time to fit residues: 179.4561 Evaluate side-chains 224 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN D 332 ASN H 9 ASN H 35 HIS E 282 GLN E 327 ASN F 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105021 restraints weight = 18586.461| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.23 r_work: 0.3107 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19517 Z= 0.162 Angle : 0.551 7.550 26315 Z= 0.301 Chirality : 0.046 0.156 2927 Planarity : 0.004 0.041 3393 Dihedral : 5.264 58.966 2657 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.29 % Allowed : 11.63 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.44 (0.17), residues: 2436 helix: 0.72 (0.17), residues: 884 sheet: 0.14 (0.23), residues: 528 loop : 0.19 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 107 TYR 0.017 0.002 TYR F 34 PHE 0.026 0.002 PHE H 2 TRP 0.013 0.002 TRP A 29 HIS 0.004 0.001 HIS E 349 Details of bonding type rmsd covalent geometry : bond 0.00357 (19509) covalent geometry : angle 0.54515 (26303) hydrogen bonds : bond 0.04628 ( 841) hydrogen bonds : angle 5.17885 ( 2283) metal coordination : bond 0.01165 ( 8) metal coordination : angle 3.75347 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 235 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7199 (mmmt) REVERT: C 72 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6814 (mt-10) REVERT: C 155 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: D 33 ASN cc_start: 0.8554 (t0) cc_final: 0.8102 (t0) REVERT: D 155 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: H 94 GLU cc_start: 0.8447 (tt0) cc_final: 0.8181 (tp30) REVERT: E 124 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7939 (tp30) REVERT: E 175 MET cc_start: 0.8676 (mmp) cc_final: 0.8133 (mmp) REVERT: E 282 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6421 (tm130) REVERT: F 107 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7937 (mmm-85) REVERT: F 117 MET cc_start: 0.8764 (ptt) cc_final: 0.8518 (ptt) outliers start: 27 outliers final: 15 residues processed: 239 average time/residue: 0.7248 time to fit residues: 191.9252 Evaluate side-chains 232 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 166 optimal weight: 0.0170 chunk 123 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 overall best weight: 3.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN D 199 ASN D 332 ASN H 9 ASN H 35 HIS E 258 HIS E 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103810 restraints weight = 18553.316| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.22 r_work: 0.3093 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19517 Z= 0.215 Angle : 0.607 8.244 26315 Z= 0.330 Chirality : 0.048 0.162 2927 Planarity : 0.004 0.041 3393 Dihedral : 5.454 58.176 2657 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.01 % Allowed : 10.91 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.36 (0.17), residues: 2436 helix: 0.65 (0.17), residues: 882 sheet: 0.10 (0.23), residues: 528 loop : 0.15 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 107 TYR 0.020 0.002 TYR F 34 PHE 0.029 0.002 PHE G 2 TRP 0.014 0.002 TRP A 29 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00483 (19509) covalent geometry : angle 0.60074 (26303) hydrogen bonds : bond 0.05132 ( 841) hydrogen bonds : angle 5.30780 ( 2283) metal coordination : bond 0.01444 ( 8) metal coordination : angle 4.04583 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.756 Fit side-chains REVERT: A 214 LYS cc_start: 0.7180 (mtmt) cc_final: 0.6727 (mtpt) REVERT: C 5 GLN cc_start: 0.8092 (tt0) cc_final: 0.7890 (mt0) REVERT: C 72 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: D 33 ASN cc_start: 0.8547 (t0) cc_final: 0.8093 (t0) REVERT: D 155 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: H 94 GLU cc_start: 0.8477 (tt0) cc_final: 0.8200 (tp30) REVERT: H 121 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: E 175 MET cc_start: 0.8685 (mmp) cc_final: 0.8316 (mmp) REVERT: E 242 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8695 (m) REVERT: E 320 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: F 107 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7897 (mmm-85) REVERT: F 117 MET cc_start: 0.8836 (ptt) cc_final: 0.8584 (ptt) REVERT: F 124 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7226 (pt0) REVERT: F 231 GLN cc_start: 0.6626 (mt0) cc_final: 0.6322 (mt0) REVERT: G 53 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7878 (mmm-85) outliers start: 42 outliers final: 21 residues processed: 245 average time/residue: 0.6748 time to fit residues: 183.8736 Evaluate side-chains 240 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 189 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 118 optimal weight: 0.2980 chunk 229 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 overall best weight: 3.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN D 199 ASN D 332 ASN H 9 ASN H 35 HIS E 327 ASN F 151 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103702 restraints weight = 18628.989| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.22 r_work: 0.3090 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19517 Z= 0.220 Angle : 0.616 8.373 26315 Z= 0.335 Chirality : 0.049 0.164 2927 Planarity : 0.004 0.041 3393 Dihedral : 5.483 56.048 2657 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.82 % Allowed : 11.15 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.17), residues: 2436 helix: 0.58 (0.17), residues: 882 sheet: 0.10 (0.23), residues: 538 loop : 0.13 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 107 TYR 0.020 0.002 TYR F 34 PHE 0.030 0.002 PHE G 2 TRP 0.014 0.003 TRP A 29 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00495 (19509) covalent geometry : angle 0.60981 (26303) hydrogen bonds : bond 0.05161 ( 841) hydrogen bonds : angle 5.34274 ( 2283) metal coordination : bond 0.01493 ( 8) metal coordination : angle 4.13488 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.717 Fit side-chains REVERT: A 214 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6671 (mttm) REVERT: D 33 ASN cc_start: 0.8549 (t0) cc_final: 0.8098 (t0) REVERT: D 155 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: H 94 GLU cc_start: 0.8477 (tt0) cc_final: 0.8198 (tp30) REVERT: H 121 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: E 242 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8691 (m) REVERT: E 320 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: F 107 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7951 (mmm-85) REVERT: F 117 MET cc_start: 0.8855 (ptt) cc_final: 0.8595 (ptt) REVERT: F 124 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7238 (pt0) REVERT: G 53 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7871 (mmm-85) outliers start: 38 outliers final: 21 residues processed: 239 average time/residue: 0.7103 time to fit residues: 188.3350 Evaluate side-chains 238 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 143 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 5 GLN D 332 ASN H 9 ASN H 35 HIS E 182 ASN E 258 HIS E 282 GLN E 327 ASN F 231 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102591 restraints weight = 18605.112| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.17 r_work: 0.3071 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 19517 Z= 0.309 Angle : 0.711 9.208 26315 Z= 0.385 Chirality : 0.053 0.190 2927 Planarity : 0.005 0.053 3393 Dihedral : 5.728 54.465 2657 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 11.48 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.13 (0.17), residues: 2436 helix: 0.40 (0.17), residues: 884 sheet: 0.04 (0.22), residues: 540 loop : 0.04 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 107 TYR 0.022 0.003 TYR F 34 PHE 0.034 0.003 PHE G 2 TRP 0.016 0.003 TRP A 29 HIS 0.007 0.002 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00702 (19509) covalent geometry : angle 0.70372 (26303) hydrogen bonds : bond 0.05918 ( 841) hydrogen bonds : angle 5.54830 ( 2283) metal coordination : bond 0.01917 ( 8) metal coordination : angle 4.67927 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.660 Fit side-chains REVERT: A 214 LYS cc_start: 0.7198 (mtmt) cc_final: 0.6753 (mtpp) REVERT: A 235 LYS cc_start: 0.7498 (mmmt) cc_final: 0.7239 (mmmt) REVERT: C 72 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: D 33 ASN cc_start: 0.8557 (t0) cc_final: 0.8141 (t0) REVERT: D 155 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: H 94 GLU cc_start: 0.8482 (tt0) cc_final: 0.8233 (tp30) REVERT: H 121 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: E 124 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7541 (mp0) REVERT: E 231 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.5842 (mt0) REVERT: E 242 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8729 (m) REVERT: E 282 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.6505 (tm130) REVERT: E 320 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: F 107 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7980 (mmm-85) REVERT: F 117 MET cc_start: 0.8914 (ptt) cc_final: 0.8656 (ptt) REVERT: G 53 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7855 (mmm-85) outliers start: 39 outliers final: 22 residues processed: 241 average time/residue: 0.6770 time to fit residues: 181.2335 Evaluate side-chains 241 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN C 5 GLN D 199 ASN D 332 ASN H 9 ASN E 327 ASN F 231 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105769 restraints weight = 18590.408| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.23 r_work: 0.3118 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19517 Z= 0.134 Angle : 0.539 7.312 26315 Z= 0.293 Chirality : 0.045 0.160 2927 Planarity : 0.003 0.040 3393 Dihedral : 5.109 46.384 2657 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 12.15 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.36 (0.17), residues: 2436 helix: 0.69 (0.17), residues: 884 sheet: 0.09 (0.23), residues: 526 loop : 0.12 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 107 TYR 0.016 0.001 TYR F 34 PHE 0.025 0.001 PHE H 2 TRP 0.014 0.002 TRP A 29 HIS 0.004 0.001 HIS E 349 Details of bonding type rmsd covalent geometry : bond 0.00285 (19509) covalent geometry : angle 0.53302 (26303) hydrogen bonds : bond 0.04369 ( 841) hydrogen bonds : angle 5.18592 ( 2283) metal coordination : bond 0.01005 ( 8) metal coordination : angle 3.91390 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 214 LYS cc_start: 0.7100 (mtmt) cc_final: 0.6660 (mtpp) REVERT: C 72 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: C 155 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: C 254 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 33 ASN cc_start: 0.8552 (t0) cc_final: 0.8109 (t0) REVERT: D 155 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: H 94 GLU cc_start: 0.8457 (tt0) cc_final: 0.8173 (tp30) REVERT: E 231 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5555 (mt0) REVERT: E 242 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8633 (m) REVERT: F 107 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7864 (mmm-85) REVERT: F 124 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7182 (pt0) outliers start: 27 outliers final: 16 residues processed: 233 average time/residue: 0.7076 time to fit residues: 183.1789 Evaluate side-chains 229 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 136 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 199 ASN B 250 GLN C 5 GLN D 199 ASN D 332 ASN H 9 ASN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS E 282 GLN E 327 ASN F 231 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106811 restraints weight = 18421.342| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.22 r_work: 0.3129 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19517 Z= 0.124 Angle : 0.521 8.509 26315 Z= 0.282 Chirality : 0.044 0.157 2927 Planarity : 0.003 0.041 3393 Dihedral : 4.864 41.864 2653 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.39 % Allowed : 12.20 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.48 (0.17), residues: 2436 helix: 0.81 (0.17), residues: 884 sheet: 0.12 (0.23), residues: 522 loop : 0.17 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 107 TYR 0.015 0.001 TYR F 34 PHE 0.023 0.001 PHE H 2 TRP 0.012 0.002 TRP A 29 HIS 0.004 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00265 (19509) covalent geometry : angle 0.51468 (26303) hydrogen bonds : bond 0.04132 ( 841) hydrogen bonds : angle 5.06344 ( 2283) metal coordination : bond 0.00890 ( 8) metal coordination : angle 3.69760 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: C 155 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: D 33 ASN cc_start: 0.8525 (t0) cc_final: 0.8102 (t0) REVERT: D 155 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: H 94 GLU cc_start: 0.8387 (tt0) cc_final: 0.8125 (tp30) REVERT: E 242 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8620 (m) REVERT: E 282 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.6388 (tm130) REVERT: F 107 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7895 (mmm-85) REVERT: F 124 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7071 (pt0) REVERT: F 231 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6282 (tp40) outliers start: 29 outliers final: 14 residues processed: 235 average time/residue: 0.6875 time to fit residues: 179.7758 Evaluate side-chains 228 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 230 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 137 optimal weight: 0.7980 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 250 GLN C 5 GLN D 199 ASN D 332 ASN H 9 ASN E 258 HIS E 282 GLN E 327 ASN F 143 HIS F 231 GLN G 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104828 restraints weight = 18608.112| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.21 r_work: 0.3104 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19517 Z= 0.156 Angle : 0.559 8.959 26315 Z= 0.302 Chirality : 0.046 0.156 2927 Planarity : 0.004 0.041 3393 Dihedral : 4.914 36.568 2651 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.15 % Allowed : 12.58 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.46 (0.17), residues: 2436 helix: 0.76 (0.17), residues: 884 sheet: 0.15 (0.23), residues: 526 loop : 0.17 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 107 TYR 0.018 0.002 TYR F 34 PHE 0.025 0.002 PHE G 2 TRP 0.012 0.002 TRP A 29 HIS 0.005 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00342 (19509) covalent geometry : angle 0.55348 (26303) hydrogen bonds : bond 0.04489 ( 841) hydrogen bonds : angle 5.13539 ( 2283) metal coordination : bond 0.01057 ( 8) metal coordination : angle 3.86174 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 214 LYS cc_start: 0.7199 (mtmt) cc_final: 0.6656 (mttm) REVERT: C 72 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: C 155 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: D 33 ASN cc_start: 0.8553 (t0) cc_final: 0.8122 (t0) REVERT: D 155 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: H 94 GLU cc_start: 0.8430 (tt0) cc_final: 0.8165 (tp30) REVERT: E 242 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8642 (m) REVERT: F 107 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7928 (mmm-85) REVERT: F 124 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7073 (pt0) REVERT: G 56 LYS cc_start: 0.8337 (mmpt) cc_final: 0.8018 (mmtp) outliers start: 24 outliers final: 16 residues processed: 220 average time/residue: 0.6963 time to fit residues: 170.0623 Evaluate side-chains 225 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 292 LYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 371 SER Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 146 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 189 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 250 GLN C 5 GLN D 332 ASN H 9 ASN E 258 HIS E 282 GLN E 327 ASN F 143 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105728 restraints weight = 18572.344| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.21 r_work: 0.3117 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19517 Z= 0.134 Angle : 0.535 8.750 26315 Z= 0.288 Chirality : 0.045 0.156 2927 Planarity : 0.003 0.041 3393 Dihedral : 4.794 35.357 2651 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.05 % Allowed : 12.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.48 (0.17), residues: 2436 helix: 0.80 (0.17), residues: 884 sheet: 0.14 (0.23), residues: 522 loop : 0.18 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 107 TYR 0.016 0.001 TYR F 34 PHE 0.029 0.001 PHE G 2 TRP 0.012 0.002 TRP A 29 HIS 0.005 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00289 (19509) covalent geometry : angle 0.52834 (26303) hydrogen bonds : bond 0.04231 ( 841) hydrogen bonds : angle 5.07833 ( 2283) metal coordination : bond 0.00907 ( 8) metal coordination : angle 3.86967 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6668.31 seconds wall clock time: 115 minutes 4.44 seconds (6904.44 seconds total)