Starting phenix.real_space_refine on Sun Aug 24 17:12:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo8_43367/08_2025/8vo8_43367_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 140 5.16 5 C 13504 2.51 5 N 3654 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21459 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.21 Number of scatterers: 21459 At special positions: 0 Unit cell: (219.39, 107.12, 156.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 12 15.00 Mg 6 11.99 O 4143 8.00 N 3654 7.00 C 13504 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: 1.64 Conformation dependent library (CDL) restraints added in 596.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 56 sheets defined 42.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.867A pdb=" N LYS A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.600A pdb=" N GLY A 211 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.522A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.786A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.814A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.827A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.616A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.788A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.735A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.502A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.709A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.533A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.767A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.707A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 4.006A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.527A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.650A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.228A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.750A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.678A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.642A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.535A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.651A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.935A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.880A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.723A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.530A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.704A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.589A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.530A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.504A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.715A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.759A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.037A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.723A pdb=" N MET E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 353 removed outlier: 3.524A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 350 through 353' Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.280A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.618A pdb=" N TYR F 91 " --> pdb=" O HIS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.878A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.723A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.785A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.701A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.580A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 288 through 295 removed outlier: 4.316A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.525A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 332 through 336 removed outlier: 4.555A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.515A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 353 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.233A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.750A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 95 removed outlier: 3.576A pdb=" N TYR G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU G 93 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 4.063A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.670A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU G 125 " --> pdb=" O GLN G 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.523A pdb=" N ALA G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.801A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.656A pdb=" N LYS G 215 " --> pdb=" O ASP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.588A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.807A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 286 through 294 removed outlier: 3.739A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR G 294 " --> pdb=" O ARG G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.576A pdb=" N MET G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 356 removed outlier: 3.558A pdb=" N GLN G 353 " --> pdb=" O SER G 350 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP G 356 " --> pdb=" O GLN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.678A pdb=" N VAL A 94 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.803A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 115 removed outlier: 3.618A pdb=" N GLY A 113 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 155 removed outlier: 5.641A pdb=" N TYR A 152 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 166 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 217 Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AB1, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.329A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.421A pdb=" N ASN A 272 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 284 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB4, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.686A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 366 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 385 through 386 removed outlier: 3.551A pdb=" N PHE A 414 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 394 through 397 removed outlier: 4.592A pdb=" N PHE A 394 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN A 407 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 432 through 435 removed outlier: 5.807A pdb=" N TYR A 432 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 444 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 455 removed outlier: 13.598A pdb=" N VAL A 461 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N GLY A 472 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR A 469 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 479 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AC2, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.917A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.946A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.946A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.709A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.592A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.550A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AE3, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.128A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET E 132 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AE6, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AE7, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.707A pdb=" N SER E 155 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AE9, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.506A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AF2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AF3, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.652A pdb=" N TYR F 166 " --> pdb=" O TYR F 169 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.652A pdb=" N TYR F 166 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AF6, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.537A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AF8, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AF9, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AG1, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.292A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 238 through 241 923 hydrogen bonds defined for protein. 2370 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: 3.68 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6790 1.33 - 1.46: 3494 1.46 - 1.58: 11383 1.58 - 1.70: 18 1.70 - 1.82: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" N THR C 303 " pdb=" CA THR C 303 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.12e-02 7.97e+03 8.67e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" N GLU F 270 " pdb=" CA GLU F 270 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.76e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 28480 1.45 - 2.90: 961 2.90 - 4.36: 224 4.36 - 5.81: 58 5.81 - 7.26: 16 Bond angle restraints: 29739 Sorted by residual: angle pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.24e+01 angle pdb=" N ILE B 64 " pdb=" CA ILE B 64 " pdb=" C ILE B 64 " ideal model delta sigma weight residual 113.47 108.35 5.12 1.01e+00 9.80e-01 2.57e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 112.96 108.56 4.40 1.00e+00 1.00e+00 1.94e+01 angle pdb=" CA GLY F 301 " pdb=" C GLY F 301 " pdb=" O GLY F 301 " ideal model delta sigma weight residual 122.39 118.85 3.54 9.30e-01 1.16e+00 1.45e+01 angle pdb=" CA MET G 47 " pdb=" C MET G 47 " pdb=" O MET G 47 " ideal model delta sigma weight residual 121.23 117.28 3.95 1.07e+00 8.73e-01 1.37e+01 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 12175 22.17 - 44.33: 866 44.33 - 66.50: 90 66.50 - 88.66: 22 88.66 - 110.83: 7 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.83 110.83 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.55 110.55 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -169.88 109.88 1 2.00e+01 2.50e-03 3.22e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2475 0.049 - 0.098: 616 0.098 - 0.147: 176 0.147 - 0.196: 11 0.196 - 0.246: 3 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA MET G 47 " pdb=" N MET G 47 " pdb=" C MET G 47 " pdb=" CB MET G 47 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LYS G 50 " pdb=" N LYS G 50 " pdb=" C LYS G 50 " pdb=" CB LYS G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR C 303 " pdb=" N THR C 303 " pdb=" C THR C 303 " pdb=" CB THR C 303 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 163 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO F 164 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 164 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 164 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 48 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C GLY G 48 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY G 48 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN G 49 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 158 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.027 5.00e-02 4.00e+02 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 111 2.46 - 3.07: 14612 3.07 - 3.68: 32732 3.68 - 4.29: 47762 4.29 - 4.90: 79893 Nonbonded interactions: 175110 Sorted by model distance: nonbonded pdb=" O ASP B 51 " pdb=" OD1 ASP B 51 " model vdw 1.844 3.040 nonbonded pdb=" O ASN A 77 " pdb=" OD1 ASN A 77 " model vdw 1.989 3.040 nonbonded pdb=" O3B ADP G 401 " pdb="MG MG G 402 " model vdw 2.041 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.094 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.096 2.170 ... (remaining 175105 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21924 Z= 0.213 Angle : 0.682 7.260 29739 Z= 0.373 Chirality : 0.047 0.246 3281 Planarity : 0.004 0.074 3827 Dihedral : 14.800 110.826 8126 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.57 % Allowed : 3.28 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2691 helix: -0.12 (0.17), residues: 948 sheet: 0.43 (0.25), residues: 483 loop : 0.07 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 217 TYR 0.011 0.001 TYR C 166 PHE 0.021 0.001 PHE B 124 TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00423 (21924) covalent geometry : angle 0.68250 (29739) hydrogen bonds : bond 0.23452 ( 907) hydrogen bonds : angle 8.31060 ( 2370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 417 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7513 (tptt) REVERT: A 69 TYR cc_start: 0.8127 (m-80) cc_final: 0.7894 (m-80) REVERT: A 152 TYR cc_start: 0.8795 (m-80) cc_final: 0.8589 (m-80) REVERT: B 14 SER cc_start: 0.9278 (t) cc_final: 0.8892 (p) REVERT: B 101 HIS cc_start: 0.7645 (m-70) cc_final: 0.7425 (m-70) REVERT: B 166 TYR cc_start: 0.8346 (t80) cc_final: 0.8146 (t80) REVERT: B 179 ASP cc_start: 0.7809 (m-30) cc_final: 0.7279 (t70) REVERT: C 59 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8446 (tp40) REVERT: C 153 LEU cc_start: 0.8767 (tp) cc_final: 0.8481 (tt) REVERT: C 176 MET cc_start: 0.8277 (mmt) cc_final: 0.8050 (mmt) REVERT: C 198 TYR cc_start: 0.8272 (m-80) cc_final: 0.7841 (m-80) REVERT: C 328 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7835 (tttt) REVERT: C 355 MET cc_start: 0.7650 (mmt) cc_final: 0.7273 (mmm) REVERT: C 374 CYS cc_start: 0.6582 (m) cc_final: 0.6274 (m) REVERT: D 5 THR cc_start: 0.4011 (OUTLIER) cc_final: 0.3731 (p) REVERT: D 107 GLU cc_start: 0.8323 (tt0) cc_final: 0.7895 (tt0) REVERT: D 111 ASN cc_start: 0.8446 (m110) cc_final: 0.7623 (m110) REVERT: D 222 ASP cc_start: 0.7277 (t0) cc_final: 0.6850 (p0) REVERT: D 291 LYS cc_start: 0.8483 (tttm) cc_final: 0.8282 (tppt) REVERT: D 296 ASN cc_start: 0.8265 (m-40) cc_final: 0.8031 (t0) REVERT: E 52 SER cc_start: 0.8943 (p) cc_final: 0.8521 (m) REVERT: E 187 ASP cc_start: 0.8506 (m-30) cc_final: 0.7918 (m-30) REVERT: E 206 ARG cc_start: 0.7382 (ttm-80) cc_final: 0.6780 (ttp-170) REVERT: E 269 MET cc_start: 0.6594 (mtp) cc_final: 0.6350 (mtt) REVERT: E 314 GLN cc_start: 0.8056 (tt0) cc_final: 0.7603 (tt0) REVERT: F 10 CYS cc_start: 0.8190 (t) cc_final: 0.7910 (t) REVERT: F 25 ASP cc_start: 0.8031 (t0) cc_final: 0.7741 (t0) REVERT: F 47 MET cc_start: 0.1827 (mmt) cc_final: 0.1363 (mmt) REVERT: F 64 ILE cc_start: 0.8428 (pt) cc_final: 0.7932 (tt) REVERT: F 169 TYR cc_start: 0.8286 (m-80) cc_final: 0.8046 (m-80) REVERT: F 171 LEU cc_start: 0.8636 (mt) cc_final: 0.8395 (mp) REVERT: F 191 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8515 (tmmt) REVERT: F 269 MET cc_start: 0.9110 (ptp) cc_final: 0.8798 (ptm) REVERT: F 324 THR cc_start: 0.8970 (p) cc_final: 0.8459 (t) REVERT: F 356 TRP cc_start: 0.7829 (m100) cc_final: 0.7474 (m100) REVERT: G 34 ILE cc_start: 0.9095 (mt) cc_final: 0.8797 (pt) REVERT: G 107 GLU cc_start: 0.7771 (tt0) cc_final: 0.7298 (tt0) REVERT: G 123 MET cc_start: 0.9152 (tpp) cc_final: 0.8937 (tpp) REVERT: G 239 SER cc_start: 0.7886 (m) cc_final: 0.7599 (p) REVERT: G 242 LEU cc_start: 0.8273 (mt) cc_final: 0.8030 (mm) REVERT: G 269 MET cc_start: 0.8374 (mtp) cc_final: 0.8064 (mtp) outliers start: 13 outliers final: 0 residues processed: 421 average time/residue: 0.1338 time to fit residues: 86.8009 Evaluate side-chains 262 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS C 87 HIS ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099568 restraints weight = 49138.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101572 restraints weight = 30335.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102934 restraints weight = 21689.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103814 restraints weight = 17348.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104169 restraints weight = 14989.993| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21924 Z= 0.131 Angle : 0.633 8.148 29739 Z= 0.317 Chirality : 0.046 0.157 3281 Planarity : 0.004 0.054 3827 Dihedral : 7.290 98.994 3049 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.92 % Allowed : 8.43 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2691 helix: 0.04 (0.17), residues: 954 sheet: 0.49 (0.24), residues: 485 loop : 0.12 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.024 0.001 TYR E 166 PHE 0.015 0.001 PHE B 124 TRP 0.017 0.001 TRP A 491 HIS 0.006 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00296 (21924) covalent geometry : angle 0.63266 (29739) hydrogen bonds : bond 0.04241 ( 907) hydrogen bonds : angle 5.82527 ( 2370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7769 (m-30) cc_final: 0.7517 (t70) REVERT: C 40 HIS cc_start: 0.7356 (m-70) cc_final: 0.6923 (m-70) REVERT: C 176 MET cc_start: 0.8223 (mmt) cc_final: 0.7446 (mmt) REVERT: D 41 GLN cc_start: 0.7298 (pp30) cc_final: 0.6650 (pt0) REVERT: E 44 MET cc_start: 0.8175 (mmm) cc_final: 0.7966 (mmm) REVERT: E 78 ASN cc_start: 0.7528 (t0) cc_final: 0.6920 (t0) REVERT: E 176 MET cc_start: 0.7271 (tpt) cc_final: 0.6774 (mmt) REVERT: E 187 ASP cc_start: 0.7953 (m-30) cc_final: 0.7722 (m-30) REVERT: E 269 MET cc_start: 0.6478 (mtp) cc_final: 0.6122 (mtt) REVERT: F 64 ILE cc_start: 0.8275 (pt) cc_final: 0.7922 (tt) REVERT: F 292 ASP cc_start: 0.7868 (t70) cc_final: 0.7540 (t0) REVERT: F 324 THR cc_start: 0.8637 (p) cc_final: 0.8038 (t) REVERT: F 356 TRP cc_start: 0.7857 (m100) cc_final: 0.7489 (m100) REVERT: G 107 GLU cc_start: 0.7700 (tt0) cc_final: 0.7355 (tt0) REVERT: G 142 LEU cc_start: 0.9028 (mt) cc_final: 0.8788 (mt) REVERT: G 185 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (mm) REVERT: G 239 SER cc_start: 0.7567 (m) cc_final: 0.7331 (p) outliers start: 21 outliers final: 11 residues processed: 337 average time/residue: 0.1190 time to fit residues: 64.5464 Evaluate side-chains 260 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain G residue 185 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 121 optimal weight: 0.1980 chunk 43 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 185 optimal weight: 0.0050 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN B 87 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 162 ASN D 41 GLN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099542 restraints weight = 49301.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100698 restraints weight = 30457.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102094 restraints weight = 23854.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102094 restraints weight = 19092.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102332 restraints weight = 18817.173| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21924 Z= 0.122 Angle : 0.599 7.572 29739 Z= 0.296 Chirality : 0.046 0.154 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.059 97.129 3048 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.44 % Allowed : 11.80 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2691 helix: 0.15 (0.17), residues: 954 sheet: 0.46 (0.24), residues: 485 loop : 0.05 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 28 TYR 0.025 0.001 TYR A 152 PHE 0.020 0.001 PHE A 31 TRP 0.033 0.001 TRP C 340 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00284 (21924) covalent geometry : angle 0.59924 (29739) hydrogen bonds : bond 0.03573 ( 907) hydrogen bonds : angle 5.36572 ( 2370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7836 (m-30) cc_final: 0.7352 (t70) REVERT: C 176 MET cc_start: 0.8073 (mmt) cc_final: 0.7291 (mmt) REVERT: C 276 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 41 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: E 78 ASN cc_start: 0.7713 (t0) cc_final: 0.7289 (t0) REVERT: E 176 MET cc_start: 0.7371 (tpt) cc_final: 0.6867 (mmt) REVERT: E 217 CYS cc_start: 0.6933 (m) cc_final: 0.6714 (m) REVERT: E 269 MET cc_start: 0.6429 (mtp) cc_final: 0.6074 (mtt) REVERT: F 64 ILE cc_start: 0.8390 (pt) cc_final: 0.8070 (tt) REVERT: F 292 ASP cc_start: 0.7892 (t70) cc_final: 0.7597 (t0) REVERT: F 324 THR cc_start: 0.8648 (p) cc_final: 0.8044 (t) REVERT: F 356 TRP cc_start: 0.7773 (m100) cc_final: 0.7450 (m100) REVERT: G 82 MET cc_start: 0.8504 (tpt) cc_final: 0.8021 (tpt) REVERT: G 107 GLU cc_start: 0.7725 (tt0) cc_final: 0.7344 (tt0) REVERT: G 185 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8250 (mm) REVERT: G 217 CYS cc_start: 0.7621 (m) cc_final: 0.7405 (m) REVERT: G 239 SER cc_start: 0.7578 (m) cc_final: 0.7325 (p) REVERT: G 248 ILE cc_start: 0.8658 (pt) cc_final: 0.8409 (pt) REVERT: G 269 MET cc_start: 0.8007 (mtp) cc_final: 0.7637 (mtp) REVERT: G 291 LYS cc_start: 0.6555 (mmtt) cc_final: 0.5786 (mmtp) outliers start: 33 outliers final: 13 residues processed: 296 average time/residue: 0.1180 time to fit residues: 56.7117 Evaluate side-chains 263 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain G residue 185 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 46 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 126 optimal weight: 0.1980 chunk 215 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 59 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN F 101 HIS G 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089969 restraints weight = 50948.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090606 restraints weight = 33522.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090975 restraints weight = 26020.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091098 restraints weight = 23802.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092249 restraints weight = 22844.455| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 21924 Z= 0.407 Angle : 0.881 11.315 29739 Z= 0.446 Chirality : 0.056 0.233 3281 Planarity : 0.006 0.046 3827 Dihedral : 8.404 103.792 3048 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.62 % Allowed : 13.85 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2691 helix: -0.14 (0.17), residues: 918 sheet: -0.16 (0.23), residues: 515 loop : -0.36 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 147 TYR 0.023 0.002 TYR E 198 PHE 0.025 0.003 PHE D 262 TRP 0.058 0.003 TRP C 340 HIS 0.010 0.002 HIS F 173 Details of bonding type rmsd covalent geometry : bond 0.00955 (21924) covalent geometry : angle 0.88071 (29739) hydrogen bonds : bond 0.05053 ( 907) hydrogen bonds : angle 5.94656 ( 2370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: B 179 ASP cc_start: 0.7996 (m-30) cc_final: 0.7663 (t70) REVERT: B 221 LEU cc_start: 0.8162 (tp) cc_final: 0.7939 (tt) REVERT: D 157 ASP cc_start: 0.7339 (p0) cc_final: 0.6930 (p0) REVERT: D 196 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7433 (mtt180) REVERT: D 253 GLU cc_start: 0.7932 (mp0) cc_final: 0.7533 (mp0) REVERT: E 81 ASP cc_start: 0.5289 (m-30) cc_final: 0.4697 (m-30) REVERT: E 176 MET cc_start: 0.7459 (tpt) cc_final: 0.6898 (tpp) REVERT: E 206 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7286 (ttp-170) REVERT: E 269 MET cc_start: 0.6860 (mtp) cc_final: 0.6338 (mtt) REVERT: F 64 ILE cc_start: 0.8541 (pt) cc_final: 0.8161 (tt) REVERT: F 324 THR cc_start: 0.8865 (p) cc_final: 0.8395 (t) REVERT: G 65 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7809 (pp) REVERT: G 82 MET cc_start: 0.8638 (tpt) cc_final: 0.8051 (tpt) REVERT: G 185 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8442 (mm) outliers start: 60 outliers final: 33 residues processed: 284 average time/residue: 0.1250 time to fit residues: 57.0372 Evaluate side-chains 247 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 283 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 235 optimal weight: 0.0000 chunk 46 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095181 restraints weight = 49809.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097033 restraints weight = 31349.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098272 restraints weight = 22916.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099081 restraints weight = 18655.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099287 restraints weight = 16291.583| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21924 Z= 0.122 Angle : 0.611 8.648 29739 Z= 0.301 Chirality : 0.046 0.174 3281 Planarity : 0.004 0.048 3827 Dihedral : 7.650 98.611 3048 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.05 % Allowed : 14.72 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2691 helix: 0.26 (0.17), residues: 918 sheet: 0.12 (0.24), residues: 469 loop : -0.18 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.012 0.001 TYR G 69 PHE 0.017 0.001 PHE A 31 TRP 0.039 0.002 TRP C 340 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00287 (21924) covalent geometry : angle 0.61096 (29739) hydrogen bonds : bond 0.03328 ( 907) hydrogen bonds : angle 5.28566 ( 2370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: B 14 SER cc_start: 0.9037 (t) cc_final: 0.8511 (p) REVERT: B 148 THR cc_start: 0.8286 (m) cc_final: 0.7886 (p) REVERT: B 179 ASP cc_start: 0.8032 (m-30) cc_final: 0.7597 (t70) REVERT: B 283 MET cc_start: 0.8523 (tpp) cc_final: 0.7952 (mpp) REVERT: C 176 MET cc_start: 0.7979 (mmt) cc_final: 0.7314 (mmt) REVERT: D 157 ASP cc_start: 0.7201 (p0) cc_final: 0.6773 (p0) REVERT: D 196 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7305 (mtt180) REVERT: E 269 MET cc_start: 0.6519 (mtp) cc_final: 0.6072 (mtt) REVERT: F 18 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7936 (mmtp) REVERT: F 64 ILE cc_start: 0.8327 (pt) cc_final: 0.8041 (tt) REVERT: F 107 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: F 145 SER cc_start: 0.9112 (t) cc_final: 0.8810 (m) REVERT: F 198 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: F 226 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: F 324 THR cc_start: 0.8644 (p) cc_final: 0.8137 (t) REVERT: G 82 MET cc_start: 0.8426 (tpt) cc_final: 0.8207 (tpt) REVERT: G 132 MET cc_start: 0.6902 (ptt) cc_final: 0.6602 (ptt) REVERT: G 185 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8384 (mm) REVERT: G 248 ILE cc_start: 0.8600 (pt) cc_final: 0.8326 (pt) REVERT: G 269 MET cc_start: 0.7964 (mtp) cc_final: 0.7712 (mtp) outliers start: 47 outliers final: 20 residues processed: 295 average time/residue: 0.1309 time to fit residues: 61.8790 Evaluate side-chains 260 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 228 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 224 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 197 optimal weight: 7.9990 chunk 111 optimal weight: 0.0050 chunk 90 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093866 restraints weight = 49581.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095708 restraints weight = 31560.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.096915 restraints weight = 23158.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097538 restraints weight = 19063.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098203 restraints weight = 16972.797| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21924 Z= 0.161 Angle : 0.630 8.861 29739 Z= 0.310 Chirality : 0.047 0.175 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.613 97.904 3048 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.05 % Allowed : 15.99 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2691 helix: 0.30 (0.17), residues: 924 sheet: 0.10 (0.24), residues: 469 loop : -0.14 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.012 0.001 TYR G 198 PHE 0.016 0.001 PHE A 31 TRP 0.027 0.002 TRP C 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00385 (21924) covalent geometry : angle 0.62990 (29739) hydrogen bonds : bond 0.03460 ( 907) hydrogen bonds : angle 5.16189 ( 2370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: B 148 THR cc_start: 0.8276 (m) cc_final: 0.7840 (p) REVERT: B 179 ASP cc_start: 0.8062 (m-30) cc_final: 0.7572 (t70) REVERT: B 283 MET cc_start: 0.8494 (tpp) cc_final: 0.7923 (mpp) REVERT: D 157 ASP cc_start: 0.7270 (p0) cc_final: 0.6800 (p0) REVERT: E 176 MET cc_start: 0.7394 (tpt) cc_final: 0.6932 (mmt) REVERT: E 269 MET cc_start: 0.6552 (mtp) cc_final: 0.6091 (mtt) REVERT: F 18 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8014 (mmtp) REVERT: F 64 ILE cc_start: 0.8346 (pt) cc_final: 0.8048 (tt) REVERT: F 107 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: F 145 SER cc_start: 0.9133 (t) cc_final: 0.8806 (m) REVERT: F 226 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: F 324 THR cc_start: 0.8646 (p) cc_final: 0.8181 (t) REVERT: G 65 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7731 (pp) REVERT: G 132 MET cc_start: 0.7122 (ptt) cc_final: 0.6781 (ptt) REVERT: G 185 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8377 (mm) REVERT: G 269 MET cc_start: 0.7978 (mtp) cc_final: 0.7688 (mtp) outliers start: 47 outliers final: 27 residues processed: 277 average time/residue: 0.1303 time to fit residues: 57.8975 Evaluate side-chains 266 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 283 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095417 restraints weight = 49257.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097275 restraints weight = 30927.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098525 restraints weight = 22663.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099171 restraints weight = 18461.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099798 restraints weight = 16387.299| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21924 Z= 0.129 Angle : 0.600 9.775 29739 Z= 0.293 Chirality : 0.046 0.171 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.439 94.680 3048 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.36 % Allowed : 16.08 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2691 helix: 0.39 (0.17), residues: 930 sheet: 0.14 (0.24), residues: 469 loop : -0.08 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.014 0.001 TYR G 198 PHE 0.015 0.001 PHE A 31 TRP 0.023 0.001 TRP C 340 HIS 0.004 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00307 (21924) covalent geometry : angle 0.59976 (29739) hydrogen bonds : bond 0.03168 ( 907) hydrogen bonds : angle 5.05022 ( 2370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: B 65 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7889 (pp) REVERT: B 148 THR cc_start: 0.8232 (m) cc_final: 0.7805 (p) REVERT: B 283 MET cc_start: 0.8400 (tpp) cc_final: 0.7913 (mpp) REVERT: C 176 MET cc_start: 0.7923 (mmt) cc_final: 0.7476 (mmt) REVERT: D 86 TRP cc_start: 0.8602 (m-10) cc_final: 0.8240 (m-10) REVERT: D 157 ASP cc_start: 0.7283 (p0) cc_final: 0.6858 (p0) REVERT: E 176 MET cc_start: 0.7354 (tpt) cc_final: 0.6896 (mmt) REVERT: E 192 ILE cc_start: 0.9373 (tp) cc_final: 0.9065 (tp) REVERT: E 269 MET cc_start: 0.6526 (mtp) cc_final: 0.6090 (mtt) REVERT: F 18 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7943 (mmtp) REVERT: F 64 ILE cc_start: 0.8329 (pt) cc_final: 0.8045 (tt) REVERT: F 107 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: F 145 SER cc_start: 0.9076 (t) cc_final: 0.8798 (m) REVERT: F 198 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: F 226 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: F 324 THR cc_start: 0.8663 (p) cc_final: 0.8189 (t) REVERT: G 65 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7656 (pp) REVERT: G 185 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (mm) REVERT: G 269 MET cc_start: 0.7976 (mtp) cc_final: 0.7651 (mtp) outliers start: 54 outliers final: 32 residues processed: 282 average time/residue: 0.1276 time to fit residues: 57.8005 Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Chi-restraints excluded: chain G residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 90 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 104 optimal weight: 0.0070 chunk 212 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN G 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.112217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.096418 restraints weight = 49237.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097276 restraints weight = 31386.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097933 restraints weight = 24389.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098493 restraints weight = 20924.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098604 restraints weight = 19889.985| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21924 Z= 0.121 Angle : 0.600 10.662 29739 Z= 0.291 Chirality : 0.046 0.169 3281 Planarity : 0.004 0.058 3827 Dihedral : 7.293 92.605 3048 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.18 % Allowed : 16.60 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2691 helix: 0.48 (0.18), residues: 930 sheet: 0.15 (0.24), residues: 469 loop : -0.02 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.012 0.001 TYR G 198 PHE 0.014 0.001 PHE A 31 TRP 0.022 0.001 TRP C 340 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00287 (21924) covalent geometry : angle 0.60025 (29739) hydrogen bonds : bond 0.03084 ( 907) hydrogen bonds : angle 4.93001 ( 2370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: B 65 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7920 (pp) REVERT: B 148 THR cc_start: 0.8257 (m) cc_final: 0.7818 (p) REVERT: B 175 ILE cc_start: 0.9004 (mt) cc_final: 0.8798 (mt) REVERT: B 176 MET cc_start: 0.6953 (ptm) cc_final: 0.6733 (ptt) REVERT: B 283 MET cc_start: 0.8345 (tpp) cc_final: 0.7892 (mpp) REVERT: D 86 TRP cc_start: 0.8562 (m-10) cc_final: 0.8142 (m-10) REVERT: D 157 ASP cc_start: 0.7336 (p0) cc_final: 0.6909 (p0) REVERT: E 176 MET cc_start: 0.7355 (tpt) cc_final: 0.6901 (mmt) REVERT: E 192 ILE cc_start: 0.9415 (tp) cc_final: 0.9135 (tp) REVERT: E 269 MET cc_start: 0.6506 (mtp) cc_final: 0.6099 (mtt) REVERT: F 18 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7822 (mmtm) REVERT: F 64 ILE cc_start: 0.8393 (pt) cc_final: 0.8130 (tt) REVERT: F 107 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: F 198 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: F 226 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: F 324 THR cc_start: 0.8673 (p) cc_final: 0.8233 (t) REVERT: G 65 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7632 (pp) REVERT: G 185 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (mm) REVERT: G 269 MET cc_start: 0.7956 (mtp) cc_final: 0.7628 (mtp) outliers start: 50 outliers final: 27 residues processed: 290 average time/residue: 0.1193 time to fit residues: 56.0888 Evaluate side-chains 277 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 113 optimal weight: 0.5980 chunk 182 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.092777 restraints weight = 49796.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.093634 restraints weight = 32791.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094442 restraints weight = 25519.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094955 restraints weight = 21548.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095069 restraints weight = 20958.815| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21924 Z= 0.226 Angle : 0.685 10.889 29739 Z= 0.337 Chirality : 0.049 0.225 3281 Planarity : 0.004 0.052 3827 Dihedral : 7.758 100.243 3048 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.27 % Allowed : 16.91 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2691 helix: 0.34 (0.17), residues: 930 sheet: 0.00 (0.24), residues: 469 loop : -0.19 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 147 TYR 0.014 0.002 TYR F 169 PHE 0.015 0.001 PHE A 31 TRP 0.020 0.002 TRP C 340 HIS 0.006 0.001 HIS F 173 Details of bonding type rmsd covalent geometry : bond 0.00536 (21924) covalent geometry : angle 0.68483 (29739) hydrogen bonds : bond 0.03680 ( 907) hydrogen bonds : angle 5.17126 ( 2370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: B 65 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7933 (pp) REVERT: B 148 THR cc_start: 0.8322 (m) cc_final: 0.7867 (p) REVERT: B 283 MET cc_start: 0.8419 (tpp) cc_final: 0.7867 (mpp) REVERT: D 157 ASP cc_start: 0.7550 (p0) cc_final: 0.7061 (p0) REVERT: E 192 ILE cc_start: 0.9403 (tp) cc_final: 0.9129 (tp) REVERT: E 283 MET cc_start: 0.8025 (mmm) cc_final: 0.7597 (mtt) REVERT: F 18 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8127 (mmtm) REVERT: F 64 ILE cc_start: 0.8471 (pt) cc_final: 0.8150 (tt) REVERT: F 107 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: F 198 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: F 226 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: F 324 THR cc_start: 0.8833 (p) cc_final: 0.8399 (t) REVERT: G 65 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (pp) REVERT: G 185 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8425 (mm) REVERT: G 269 MET cc_start: 0.8153 (mtp) cc_final: 0.7856 (mtp) outliers start: 52 outliers final: 36 residues processed: 275 average time/residue: 0.1170 time to fit residues: 52.1585 Evaluate side-chains 272 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Chi-restraints excluded: chain G residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094756 restraints weight = 49515.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095615 restraints weight = 31719.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.096491 restraints weight = 24390.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096894 restraints weight = 20643.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097018 restraints weight = 20224.184| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21924 Z= 0.147 Angle : 0.640 11.405 29739 Z= 0.311 Chirality : 0.047 0.175 3281 Planarity : 0.004 0.052 3827 Dihedral : 7.591 96.146 3048 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.97 % Allowed : 17.56 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2691 helix: 0.40 (0.17), residues: 930 sheet: 0.01 (0.24), residues: 469 loop : -0.13 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 118 TYR 0.016 0.001 TYR G 198 PHE 0.013 0.001 PHE A 31 TRP 0.021 0.001 TRP C 340 HIS 0.004 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00353 (21924) covalent geometry : angle 0.64022 (29739) hydrogen bonds : bond 0.03260 ( 907) hydrogen bonds : angle 5.03308 ( 2370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: B 65 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7853 (pp) REVERT: B 148 THR cc_start: 0.8255 (m) cc_final: 0.7833 (p) REVERT: B 283 MET cc_start: 0.8315 (tpp) cc_final: 0.7838 (mpp) REVERT: C 221 LEU cc_start: 0.7832 (mm) cc_final: 0.7556 (mm) REVERT: D 157 ASP cc_start: 0.7355 (p0) cc_final: 0.6894 (p0) REVERT: E 192 ILE cc_start: 0.9417 (tp) cc_final: 0.9153 (tp) REVERT: E 283 MET cc_start: 0.7941 (mmm) cc_final: 0.7540 (mtt) REVERT: F 18 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7921 (mmtm) REVERT: F 64 ILE cc_start: 0.8400 (pt) cc_final: 0.8121 (tt) REVERT: F 107 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: F 198 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: F 226 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: F 324 THR cc_start: 0.8710 (p) cc_final: 0.8392 (t) REVERT: G 65 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7716 (pp) REVERT: G 185 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8457 (mm) REVERT: G 269 MET cc_start: 0.8068 (mtp) cc_final: 0.7748 (mtp) outliers start: 45 outliers final: 31 residues processed: 272 average time/residue: 0.1130 time to fit residues: 50.2996 Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 243 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096913 restraints weight = 49276.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098718 restraints weight = 30874.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099971 restraints weight = 22690.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100815 restraints weight = 18445.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101266 restraints weight = 16081.523| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21924 Z= 0.109 Angle : 0.609 11.837 29739 Z= 0.294 Chirality : 0.045 0.166 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.235 90.677 3048 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.62 % Allowed : 17.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2691 helix: 0.51 (0.18), residues: 924 sheet: 0.12 (0.24), residues: 469 loop : 0.04 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.012 0.001 TYR G 198 PHE 0.011 0.001 PHE F 352 TRP 0.021 0.001 TRP C 340 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00256 (21924) covalent geometry : angle 0.60884 (29739) hydrogen bonds : bond 0.02927 ( 907) hydrogen bonds : angle 4.86878 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2806.49 seconds wall clock time: 49 minutes 38.19 seconds (2978.19 seconds total)