Starting phenix.real_space_refine on Wed Jun 18 19:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo8_43367/06_2025/8vo8_43367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo8_43367/06_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_43367/06_2025/8vo8_43367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo8_43367/06_2025/8vo8_43367.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo8_43367/06_2025/8vo8_43367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo8_43367/06_2025/8vo8_43367_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.38, per 1000 atoms: 0.67 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: 6.88 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 4.22 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: 13.37 Time building geometry restraints manager: 8.00 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: 9.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 62.940 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.220 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:4.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.890 ------------------------------------------------------------------------------- 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 : 14.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS A 65 PHE 0.021 0.001 PHE B 124 TYR 0.011 0.001 TYR C 166 ARG 0.012 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.23452 ( 907) hydrogen bonds : angle 8.31060 ( 2370) covalent geometry : bond 0.00423 (21924) covalent geometry : angle 0.68250 (29739) *********************** 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 : 2.328 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: 0.3509 time to fit residues: 224.9804 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 : 2.672 ------------------------------------------------------------------------------- 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 227 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097449 restraints weight = 49390.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098770 restraints weight = 30739.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100694 restraints weight = 21834.802| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1607 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= 0.180 Angle : 0.667 8.372 29739 Z= 0.335 Chirality : 0.048 0.158 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.532 102.171 3049 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.05 % Allowed : 8.96 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2691 helix: 0.00 (0.17), residues: 960 sheet: 0.39 (0.24), residues: 484 loop : -0.04 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 491 HIS 0.006 0.001 HIS C 87 PHE 0.014 0.001 PHE A 31 TYR 0.027 0.001 TYR E 166 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 907) hydrogen bonds : angle 5.92091 ( 2370) covalent geometry : bond 0.00423 (21924) covalent geometry : angle 0.66652 (29739) *********************** 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 325 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7850 (m-30) cc_final: 0.7601 (t70) REVERT: C 40 HIS cc_start: 0.7210 (m-70) cc_final: 0.6830 (m-70) REVERT: C 153 LEU cc_start: 0.9073 (tp) cc_final: 0.8860 (tt) REVERT: C 374 CYS cc_start: 0.6808 (m) cc_final: 0.6484 (m) REVERT: D 41 GLN cc_start: 0.7365 (pp30) cc_final: 0.6734 (pt0) REVERT: D 157 ASP cc_start: 0.7180 (p0) cc_final: 0.6821 (p0) REVERT: E 78 ASN cc_start: 0.7604 (t0) cc_final: 0.7058 (t0) REVERT: E 176 MET cc_start: 0.7369 (tpt) cc_final: 0.6834 (mmt) REVERT: E 187 ASP cc_start: 0.8040 (m-30) cc_final: 0.7647 (m-30) REVERT: E 206 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7390 (ttp80) REVERT: E 269 MET cc_start: 0.6418 (mtp) cc_final: 0.6040 (mtt) REVERT: F 25 ASP cc_start: 0.7862 (t0) cc_final: 0.7596 (t0) REVERT: F 64 ILE cc_start: 0.8304 (pt) cc_final: 0.7972 (tt) REVERT: F 292 ASP cc_start: 0.7833 (t70) cc_final: 0.7564 (t0) REVERT: F 324 THR cc_start: 0.8612 (p) cc_final: 0.8008 (t) REVERT: F 356 TRP cc_start: 0.7882 (m100) cc_final: 0.7586 (m100) REVERT: G 107 GLU cc_start: 0.7755 (tt0) cc_final: 0.7381 (tt0) REVERT: G 142 LEU cc_start: 0.9095 (mt) cc_final: 0.8871 (mt) REVERT: G 185 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8340 (mm) REVERT: G 239 SER cc_start: 0.7582 (m) cc_final: 0.7351 (p) outliers start: 24 outliers final: 13 residues processed: 315 average time/residue: 0.3085 time to fit residues: 153.9644 Evaluate side-chains 257 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU 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 6 THR 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 14 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 162 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 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 = 0.3620 r_free = 0.3620 target = 0.111376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094748 restraints weight = 49595.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096618 restraints weight = 31129.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097882 restraints weight = 22788.607| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21924 Z= 0.196 Angle : 0.656 8.051 29739 Z= 0.328 Chirality : 0.048 0.163 3281 Planarity : 0.004 0.042 3827 Dihedral : 7.568 102.912 3048 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.62 % Allowed : 12.19 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2691 helix: 0.16 (0.17), residues: 918 sheet: 0.23 (0.24), residues: 479 loop : -0.04 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 340 HIS 0.006 0.001 HIS B 371 PHE 0.021 0.001 PHE A 31 TYR 0.022 0.001 TYR A 152 ARG 0.005 0.001 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 907) hydrogen bonds : angle 5.54954 ( 2370) covalent geometry : bond 0.00464 (21924) covalent geometry : angle 0.65572 (29739) *********************** 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 297 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7780 (mtp) cc_final: 0.7564 (mtp) REVERT: B 179 ASP cc_start: 0.7958 (m-30) cc_final: 0.7577 (t70) REVERT: D 41 GLN cc_start: 0.7220 (pp30) cc_final: 0.6809 (pt0) REVERT: D 157 ASP cc_start: 0.7286 (p0) cc_final: 0.6853 (p0) REVERT: E 176 MET cc_start: 0.7423 (tpt) cc_final: 0.6897 (mmt) REVERT: E 187 ASP cc_start: 0.8057 (m-30) cc_final: 0.7819 (m-30) REVERT: E 217 CYS cc_start: 0.7300 (m) cc_final: 0.6944 (m) REVERT: E 269 MET cc_start: 0.6585 (mtp) cc_final: 0.6058 (mtt) REVERT: F 64 ILE cc_start: 0.8473 (pt) cc_final: 0.8110 (tt) REVERT: F 145 SER cc_start: 0.9353 (t) cc_final: 0.9067 (m) REVERT: F 292 ASP cc_start: 0.7954 (t70) cc_final: 0.7666 (t0) REVERT: F 324 THR cc_start: 0.8767 (p) cc_final: 0.8246 (t) REVERT: G 82 MET cc_start: 0.8584 (tpt) cc_final: 0.7995 (tpt) REVERT: G 185 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8387 (mm) REVERT: G 313 MET cc_start: 0.8531 (mtp) cc_final: 0.8331 (mtp) outliers start: 37 outliers final: 20 residues processed: 290 average time/residue: 0.3054 time to fit residues: 142.4591 Evaluate side-chains 254 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 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 212 ILE 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 F residue 265 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 72 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 140 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 266 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.0242 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.113215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096708 restraints weight = 49877.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098613 restraints weight = 31330.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099895 restraints weight = 22809.563| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21924 Z= 0.127 Angle : 0.602 7.985 29739 Z= 0.295 Chirality : 0.046 0.154 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.324 97.251 3048 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.88 % Allowed : 13.63 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2691 helix: 0.34 (0.17), residues: 918 sheet: 0.27 (0.24), residues: 484 loop : 0.04 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.019 0.001 PHE A 31 TYR 0.022 0.001 TYR A 152 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 907) hydrogen bonds : angle 5.23768 ( 2370) covalent geometry : bond 0.00299 (21924) covalent geometry : angle 0.60213 (29739) *********************** 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 313 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: B 14 SER cc_start: 0.9041 (t) cc_final: 0.8627 (p) REVERT: B 148 THR cc_start: 0.8294 (m) cc_final: 0.7856 (p) REVERT: B 179 ASP cc_start: 0.7918 (m-30) cc_final: 0.7568 (t70) REVERT: C 169 TYR cc_start: 0.8442 (m-80) cc_final: 0.8222 (m-80) REVERT: C 374 CYS cc_start: 0.7145 (m) cc_final: 0.6772 (m) REVERT: D 41 GLN cc_start: 0.7084 (pp30) cc_final: 0.6706 (pt0) REVERT: D 157 ASP cc_start: 0.7196 (p0) cc_final: 0.6828 (p0) REVERT: D 253 GLU cc_start: 0.7875 (mp0) cc_final: 0.7625 (mp0) REVERT: E 269 MET cc_start: 0.6538 (mtp) cc_final: 0.6048 (mtt) REVERT: F 64 ILE cc_start: 0.8348 (pt) cc_final: 0.8032 (tt) REVERT: F 145 SER cc_start: 0.9248 (t) cc_final: 0.8933 (m) REVERT: F 292 ASP cc_start: 0.7809 (t70) cc_final: 0.7600 (t0) REVERT: F 324 THR cc_start: 0.8689 (p) cc_final: 0.8126 (t) REVERT: G 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8077 (tpt) REVERT: G 185 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8346 (mm) REVERT: G 239 SER cc_start: 0.7667 (m) cc_final: 0.7433 (p) REVERT: G 248 ILE cc_start: 0.8612 (pt) cc_final: 0.8400 (pt) outliers start: 43 outliers final: 20 residues processed: 301 average time/residue: 0.3422 time to fit residues: 167.9577 Evaluate side-chains 264 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 129 VAL 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 41 GLN 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 F residue 10 CYS Chi-restraints excluded: chain F residue 54 VAL 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 149 THR Chi-restraints excluded: chain G residue 185 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 101 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093915 restraints weight = 49710.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094793 restraints weight = 32090.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095544 restraints weight = 25471.986| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21924 Z= 0.226 Angle : 0.674 8.459 29739 Z= 0.334 Chirality : 0.048 0.162 3281 Planarity : 0.004 0.045 3827 Dihedral : 7.665 101.837 3048 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.45 % Allowed : 14.98 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2691 helix: 0.25 (0.17), residues: 924 sheet: 0.08 (0.24), residues: 479 loop : -0.11 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 340 HIS 0.005 0.001 HIS F 173 PHE 0.019 0.001 PHE A 31 TYR 0.018 0.002 TYR A 152 ARG 0.006 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 907) hydrogen bonds : angle 5.30863 ( 2370) covalent geometry : bond 0.00535 (21924) covalent geometry : angle 0.67355 (29739) *********************** 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 299 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: B 179 ASP cc_start: 0.8005 (m-30) cc_final: 0.7669 (t70) REVERT: C 169 TYR cc_start: 0.8561 (m-80) cc_final: 0.8351 (m-80) REVERT: D 157 ASP cc_start: 0.7358 (p0) cc_final: 0.6874 (p0) REVERT: E 176 MET cc_start: 0.7436 (tpt) cc_final: 0.6961 (mmt) REVERT: E 269 MET cc_start: 0.6557 (mtp) cc_final: 0.6059 (mtt) REVERT: F 18 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8039 (mmtm) REVERT: F 64 ILE cc_start: 0.8458 (pt) cc_final: 0.8128 (tt) REVERT: F 145 SER cc_start: 0.9249 (t) cc_final: 0.8901 (m) REVERT: F 292 ASP cc_start: 0.7878 (t70) cc_final: 0.7674 (t0) REVERT: F 324 THR cc_start: 0.8699 (p) cc_final: 0.8200 (t) REVERT: G 82 MET cc_start: 0.8530 (tpt) cc_final: 0.8113 (tpt) REVERT: G 185 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (mm) outliers start: 56 outliers final: 39 residues processed: 284 average time/residue: 0.4202 time to fit residues: 191.7214 Evaluate side-chains 268 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 318 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU 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 89 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 10 CYS 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 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 E residue 267 ILE Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 226 GLU 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 72 GLU Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 149 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 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 216 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097407 restraints weight = 49023.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098483 restraints weight = 30717.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099801 restraints weight = 23744.029| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21924 Z= 0.113 Angle : 0.597 9.086 29739 Z= 0.292 Chirality : 0.045 0.151 3281 Planarity : 0.004 0.047 3827 Dihedral : 7.339 94.793 3048 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.97 % Allowed : 15.95 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2691 helix: 0.36 (0.17), residues: 924 sheet: 0.25 (0.24), residues: 469 loop : 0.06 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.016 0.001 PHE A 31 TYR 0.016 0.001 TYR G 198 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 907) hydrogen bonds : angle 5.07016 ( 2370) covalent geometry : bond 0.00265 (21924) covalent geometry : angle 0.59685 (29739) *********************** 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 308 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: B 148 THR cc_start: 0.8255 (m) cc_final: 0.7880 (p) REVERT: B 178 LEU cc_start: 0.8583 (tp) cc_final: 0.8381 (tp) REVERT: B 179 ASP cc_start: 0.8010 (m-30) cc_final: 0.7544 (t70) REVERT: B 283 MET cc_start: 0.8441 (tpp) cc_final: 0.7884 (mpp) REVERT: C 169 TYR cc_start: 0.8453 (m-80) cc_final: 0.8214 (m-80) REVERT: C 176 MET cc_start: 0.7909 (mmt) cc_final: 0.7398 (mmt) REVERT: C 374 CYS cc_start: 0.7180 (m) cc_final: 0.6727 (m) REVERT: D 157 ASP cc_start: 0.7435 (p0) cc_final: 0.6969 (p0) REVERT: E 192 ILE cc_start: 0.9378 (tp) cc_final: 0.9034 (tp) REVERT: E 217 CYS cc_start: 0.7118 (m) cc_final: 0.6912 (m) REVERT: E 269 MET cc_start: 0.6520 (mtp) cc_final: 0.6088 (mtt) REVERT: F 64 ILE cc_start: 0.8343 (pt) cc_final: 0.8055 (tt) REVERT: F 145 SER cc_start: 0.9141 (t) cc_final: 0.8834 (m) REVERT: F 198 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: F 324 THR cc_start: 0.8638 (p) cc_final: 0.8147 (t) REVERT: G 143 TYR cc_start: 0.7190 (m-80) cc_final: 0.6897 (m-80) REVERT: G 185 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 45 outliers final: 22 residues processed: 295 average time/residue: 0.2959 time to fit residues: 140.9038 Evaluate side-chains 269 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 65 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 299 MET Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 149 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 136 optimal weight: 0.0040 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 225 ASN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.114282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097867 restraints weight = 48882.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099751 restraints weight = 30389.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101036 restraints weight = 22163.514| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21924 Z= 0.106 Angle : 0.588 10.388 29739 Z= 0.286 Chirality : 0.045 0.158 3281 Planarity : 0.004 0.047 3827 Dihedral : 7.107 92.101 3048 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.88 % Allowed : 16.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2691 helix: 0.46 (0.18), residues: 918 sheet: 0.27 (0.24), residues: 469 loop : 0.10 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.014 0.001 PHE A 31 TYR 0.018 0.001 TYR D 198 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 907) hydrogen bonds : angle 4.91676 ( 2370) covalent geometry : bond 0.00249 (21924) covalent geometry : angle 0.58824 (29739) *********************** 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 309 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: B 175 ILE cc_start: 0.9037 (mt) cc_final: 0.8819 (mt) REVERT: B 179 ASP cc_start: 0.8028 (m-30) cc_final: 0.7560 (t70) REVERT: B 283 MET cc_start: 0.8314 (tpp) cc_final: 0.7796 (mpp) REVERT: C 149 THR cc_start: 0.8535 (p) cc_final: 0.8268 (t) REVERT: C 169 TYR cc_start: 0.8390 (m-80) cc_final: 0.8172 (m-80) REVERT: C 176 MET cc_start: 0.7971 (mmt) cc_final: 0.7538 (mmt) REVERT: C 374 CYS cc_start: 0.7171 (m) cc_final: 0.6865 (m) REVERT: D 157 ASP cc_start: 0.7321 (p0) cc_final: 0.6855 (p0) REVERT: E 192 ILE cc_start: 0.9397 (tp) cc_final: 0.9062 (tp) REVERT: E 269 MET cc_start: 0.6521 (mtp) cc_final: 0.6057 (mtt) REVERT: F 64 ILE cc_start: 0.8342 (pt) cc_final: 0.8067 (tt) REVERT: F 145 SER cc_start: 0.9116 (t) cc_final: 0.8787 (m) REVERT: F 198 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: F 324 THR cc_start: 0.8654 (p) cc_final: 0.8171 (t) REVERT: G 143 TYR cc_start: 0.7175 (m-80) cc_final: 0.6916 (m-80) REVERT: G 185 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8411 (mm) REVERT: G 354 GLN cc_start: 0.7069 (tp40) cc_final: 0.6859 (tp-100) outliers start: 43 outliers final: 21 residues processed: 296 average time/residue: 0.3261 time to fit residues: 158.9890 Evaluate side-chains 271 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU 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 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 41 GLN 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 F residue 198 TYR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3630 r_free = 0.3630 target = 0.111996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095309 restraints weight = 49441.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097163 restraints weight = 31174.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098436 restraints weight = 22861.214| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21924 Z= 0.158 Angle : 0.624 10.390 29739 Z= 0.305 Chirality : 0.046 0.158 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.252 96.112 3048 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.97 % Allowed : 17.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2691 helix: 0.48 (0.18), residues: 918 sheet: 0.25 (0.24), residues: 469 loop : 0.03 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.014 0.001 PHE A 31 TYR 0.012 0.001 TYR D 198 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 907) hydrogen bonds : angle 4.95787 ( 2370) covalent geometry : bond 0.00376 (21924) covalent geometry : angle 0.62391 (29739) *********************** 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 291 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: B 283 MET cc_start: 0.8329 (tpp) cc_final: 0.7858 (mpp) REVERT: C 149 THR cc_start: 0.8615 (p) cc_final: 0.8281 (t) REVERT: C 169 TYR cc_start: 0.8451 (m-80) cc_final: 0.8222 (m-80) REVERT: C 374 CYS cc_start: 0.7189 (m) cc_final: 0.6671 (m) REVERT: D 157 ASP cc_start: 0.7335 (p0) cc_final: 0.6861 (p0) REVERT: E 192 ILE cc_start: 0.9404 (tp) cc_final: 0.9130 (tp) REVERT: E 269 MET cc_start: 0.6570 (mtp) cc_final: 0.6120 (mtt) REVERT: F 64 ILE cc_start: 0.8403 (pt) cc_final: 0.8108 (tt) REVERT: F 107 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6955 (tm-30) REVERT: F 145 SER cc_start: 0.9150 (t) cc_final: 0.8828 (m) REVERT: F 198 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: F 226 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: F 324 THR cc_start: 0.8674 (p) cc_final: 0.8216 (t) REVERT: G 185 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8406 (mm) outliers start: 45 outliers final: 33 residues processed: 276 average time/residue: 0.3074 time to fit residues: 137.3935 Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 149 THR 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 180 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 8 LEU 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 339 VAL Chi-restraints excluded: chain E residue 41 GLN 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 247 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 85 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 9 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 260 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 174 optimal weight: 0.1980 chunk 177 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.114007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097413 restraints weight = 48705.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099380 restraints weight = 30101.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100685 restraints weight = 21717.257| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21924 Z= 0.112 Angle : 0.596 10.915 29739 Z= 0.289 Chirality : 0.045 0.154 3281 Planarity : 0.004 0.047 3827 Dihedral : 7.069 91.407 3048 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.88 % Allowed : 17.61 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2691 helix: 0.53 (0.18), residues: 918 sheet: 0.26 (0.24), residues: 469 loop : 0.13 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.013 0.001 PHE A 31 TYR 0.010 0.001 TYR G 198 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 907) hydrogen bonds : angle 4.85097 ( 2370) covalent geometry : bond 0.00265 (21924) covalent geometry : angle 0.59620 (29739) *********************** 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 296 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: B 283 MET cc_start: 0.8319 (tpp) cc_final: 0.7867 (mpp) REVERT: C 149 THR cc_start: 0.8622 (p) cc_final: 0.8296 (t) REVERT: C 169 TYR cc_start: 0.8454 (m-80) cc_final: 0.8217 (m-80) REVERT: C 176 MET cc_start: 0.7977 (mmt) cc_final: 0.7543 (mmt) REVERT: C 198 TYR cc_start: 0.8110 (m-10) cc_final: 0.7858 (m-80) REVERT: C 374 CYS cc_start: 0.7214 (m) cc_final: 0.6788 (m) REVERT: D 157 ASP cc_start: 0.7446 (p0) cc_final: 0.6984 (p0) REVERT: E 192 ILE cc_start: 0.9422 (tp) cc_final: 0.9116 (tp) REVERT: E 269 MET cc_start: 0.6614 (mtp) cc_final: 0.6116 (mtt) REVERT: F 64 ILE cc_start: 0.8503 (pt) cc_final: 0.8197 (tt) REVERT: F 107 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7217 (tm-30) REVERT: F 145 SER cc_start: 0.9127 (t) cc_final: 0.8832 (m) REVERT: F 198 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: F 226 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: F 324 THR cc_start: 0.8731 (p) cc_final: 0.8310 (t) REVERT: G 143 TYR cc_start: 0.7325 (m-80) cc_final: 0.7002 (m-80) REVERT: G 185 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (mm) outliers start: 43 outliers final: 28 residues processed: 279 average time/residue: 0.3037 time to fit residues: 137.4383 Evaluate side-chains 272 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 MET 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 180 LEU Chi-restraints excluded: chain C residue 202 THR 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 D residue 294 TYR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 41 GLN 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 F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 283 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 173 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 185 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097308 restraints weight = 49006.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099218 restraints weight = 30399.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100474 restraints weight = 22065.118| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21924 Z= 0.117 Angle : 0.603 11.231 29739 Z= 0.291 Chirality : 0.045 0.163 3281 Planarity : 0.004 0.047 3827 Dihedral : 7.019 91.230 3048 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.70 % Allowed : 17.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2691 helix: 0.55 (0.18), residues: 918 sheet: 0.24 (0.24), residues: 469 loop : 0.15 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.013 0.001 PHE A 31 TYR 0.020 0.001 TYR F 337 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 907) hydrogen bonds : angle 4.79936 ( 2370) covalent geometry : bond 0.00279 (21924) covalent geometry : angle 0.60261 (29739) ********************** 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 290 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.7647 (m-10) cc_final: 0.7411 (m-10) REVERT: A 292 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: B 148 THR cc_start: 0.8058 (m) cc_final: 0.7575 (p) REVERT: B 283 MET cc_start: 0.8277 (tpp) cc_final: 0.7851 (mpp) REVERT: C 149 THR cc_start: 0.8579 (p) cc_final: 0.8294 (t) REVERT: C 169 TYR cc_start: 0.8413 (m-80) cc_final: 0.8200 (m-80) REVERT: C 198 TYR cc_start: 0.8084 (m-10) cc_final: 0.7794 (m-80) REVERT: C 374 CYS cc_start: 0.7072 (m) cc_final: 0.6689 (m) REVERT: D 157 ASP cc_start: 0.7478 (p0) cc_final: 0.7012 (p0) REVERT: E 192 ILE cc_start: 0.9420 (tp) cc_final: 0.9128 (tp) REVERT: E 269 MET cc_start: 0.6519 (mtp) cc_final: 0.6051 (mtt) REVERT: E 283 MET cc_start: 0.7953 (mmm) cc_final: 0.7493 (mtt) REVERT: F 64 ILE cc_start: 0.8401 (pt) cc_final: 0.8137 (tt) REVERT: F 107 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7277 (tm-30) REVERT: F 198 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: F 226 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: F 324 THR cc_start: 0.8690 (p) cc_final: 0.8241 (t) REVERT: G 143 TYR cc_start: 0.7378 (m-80) cc_final: 0.7021 (m-80) REVERT: G 185 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 39 outliers final: 30 residues processed: 279 average time/residue: 0.3001 time to fit residues: 136.8936 Evaluate side-chains 279 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 MET 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 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 8 LEU 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 D residue 339 VAL Chi-restraints excluded: chain E residue 41 GLN 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 F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 257 CYS 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 14 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 283 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 16 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 247 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097672 restraints weight = 48760.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099661 restraints weight = 30140.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100965 restraints weight = 21639.532| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21924 Z= 0.110 Angle : 0.602 11.560 29739 Z= 0.287 Chirality : 0.045 0.162 3281 Planarity : 0.004 0.046 3827 Dihedral : 6.918 89.623 3048 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.92 % Allowed : 17.78 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2691 helix: 0.60 (0.18), residues: 918 sheet: 0.24 (0.24), residues: 469 loop : 0.18 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.012 0.001 PHE A 31 TYR 0.016 0.001 TYR F 337 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 907) hydrogen bonds : angle 4.76007 ( 2370) covalent geometry : bond 0.00262 (21924) covalent geometry : angle 0.60161 (29739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6812.03 seconds wall clock time: 122 minutes 5.79 seconds (7325.79 seconds total)