Starting phenix.real_space_refine on Wed May 21 15:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo8_43367/05_2025/8vo8_43367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo8_43367/05_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_43367/05_2025/8vo8_43367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo8_43367/05_2025/8vo8_43367.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo8_43367/05_2025/8vo8_43367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo8_43367/05_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.50, per 1000 atoms: 0.68 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: 5.66 Conformation dependent library (CDL) restraints added in 3.0 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: 3.53 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: 8.62 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6790 1.33 - 1.46: 3494 1.46 - 1.58: 11383 1.58 - 1.70: 18 1.70 - 1.82: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" N THR C 303 " pdb=" CA THR C 303 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.12e-02 7.97e+03 8.67e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" N GLU F 270 " pdb=" CA GLU F 270 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.76e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 28480 1.45 - 2.90: 961 2.90 - 4.36: 224 4.36 - 5.81: 58 5.81 - 7.26: 16 Bond angle restraints: 29739 Sorted by residual: angle pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.24e+01 angle pdb=" N ILE B 64 " pdb=" CA ILE B 64 " pdb=" C ILE B 64 " ideal model delta sigma weight residual 113.47 108.35 5.12 1.01e+00 9.80e-01 2.57e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 112.96 108.56 4.40 1.00e+00 1.00e+00 1.94e+01 angle pdb=" CA GLY F 301 " pdb=" C GLY F 301 " pdb=" O GLY F 301 " ideal model delta sigma weight residual 122.39 118.85 3.54 9.30e-01 1.16e+00 1.45e+01 angle pdb=" CA MET G 47 " pdb=" C MET G 47 " pdb=" O MET G 47 " ideal model delta sigma weight residual 121.23 117.28 3.95 1.07e+00 8.73e-01 1.37e+01 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 12175 22.17 - 44.33: 866 44.33 - 66.50: 90 66.50 - 88.66: 22 88.66 - 110.83: 7 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.83 110.83 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.55 110.55 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -169.88 109.88 1 2.00e+01 2.50e-03 3.22e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2475 0.049 - 0.098: 616 0.098 - 0.147: 176 0.147 - 0.196: 11 0.196 - 0.246: 3 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA MET G 47 " pdb=" N MET G 47 " pdb=" C MET G 47 " pdb=" CB MET G 47 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LYS G 50 " pdb=" N LYS G 50 " pdb=" C LYS G 50 " pdb=" CB LYS G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR C 303 " pdb=" N THR C 303 " pdb=" C THR C 303 " pdb=" CB THR C 303 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 163 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO F 164 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 164 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 164 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 48 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C GLY G 48 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY G 48 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN G 49 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 158 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.027 5.00e-02 4.00e+02 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 111 2.46 - 3.07: 14612 3.07 - 3.68: 32732 3.68 - 4.29: 47762 4.29 - 4.90: 79893 Nonbonded interactions: 175110 Sorted by model distance: nonbonded pdb=" O ASP B 51 " pdb=" OD1 ASP B 51 " model vdw 1.844 3.040 nonbonded pdb=" O ASN A 77 " pdb=" OD1 ASN A 77 " model vdw 1.989 3.040 nonbonded pdb=" O3B ADP G 401 " pdb="MG MG G 402 " model vdw 2.041 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.094 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.096 2.170 ... (remaining 175105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 53.100 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- 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 : 2.354 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: 0.3363 time to fit residues: 215.2737 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 : 2.409 ------------------------------------------------------------------------------- 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 = 0.113128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097463 restraints weight = 49368.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098517 restraints weight = 30409.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100025 restraints weight = 23323.663| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 5.92092 ( 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 : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7837 (m-30) cc_final: 0.7599 (t70) REVERT: C 40 HIS cc_start: 0.7233 (m-70) cc_final: 0.6848 (m-70) REVERT: C 153 LEU cc_start: 0.9074 (tp) cc_final: 0.8867 (tt) REVERT: C 374 CYS cc_start: 0.6844 (m) cc_final: 0.6473 (m) REVERT: D 41 GLN cc_start: 0.7377 (pp30) cc_final: 0.6748 (pt0) REVERT: D 157 ASP cc_start: 0.7229 (p0) cc_final: 0.6860 (p0) REVERT: E 44 MET cc_start: 0.8158 (mmm) cc_final: 0.7954 (mmm) REVERT: E 78 ASN cc_start: 0.7586 (t0) cc_final: 0.7039 (t0) REVERT: E 176 MET cc_start: 0.7359 (tpt) cc_final: 0.6829 (mmt) REVERT: E 187 ASP cc_start: 0.7960 (m-30) cc_final: 0.7574 (m-30) REVERT: E 206 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7378 (ttp80) REVERT: E 269 MET cc_start: 0.6419 (mtp) cc_final: 0.6044 (mtt) REVERT: F 25 ASP cc_start: 0.7877 (t0) cc_final: 0.7620 (t0) REVERT: F 64 ILE cc_start: 0.8320 (pt) cc_final: 0.7986 (tt) REVERT: F 292 ASP cc_start: 0.7828 (t70) cc_final: 0.7564 (t0) REVERT: F 324 THR cc_start: 0.8654 (p) cc_final: 0.8057 (t) REVERT: F 356 TRP cc_start: 0.7879 (m100) cc_final: 0.7578 (m100) REVERT: G 81 ASP cc_start: 0.8373 (m-30) cc_final: 0.8168 (m-30) REVERT: G 107 GLU cc_start: 0.7741 (tt0) cc_final: 0.7366 (tt0) REVERT: G 142 LEU cc_start: 0.9089 (mt) cc_final: 0.8864 (mt) REVERT: G 185 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8351 (mm) REVERT: G 239 SER cc_start: 0.7604 (m) cc_final: 0.7369 (p) outliers start: 24 outliers final: 13 residues processed: 315 average time/residue: 0.3093 time to fit residues: 153.9775 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 : 2.425 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095846 restraints weight = 49349.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097745 restraints weight = 30638.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099005 restraints weight = 22277.049| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21924 Z= 0.167 Angle : 0.632 7.867 29739 Z= 0.315 Chirality : 0.047 0.159 3281 Planarity : 0.004 0.043 3827 Dihedral : 7.435 101.682 3048 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.44 % Allowed : 12.06 % Favored : 86.50 % 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: 0.10 (0.16), residues: 2691 helix: 0.22 (0.17), residues: 918 sheet: 0.33 (0.24), residues: 484 loop : 0.01 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 340 HIS 0.007 0.001 HIS B 371 PHE 0.021 0.001 PHE A 31 TYR 0.023 0.001 TYR A 152 ARG 0.005 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 907) hydrogen bonds : angle 5.50273 ( 2370) covalent geometry : bond 0.00395 (21924) covalent geometry : angle 0.63203 (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 298 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 ASP cc_start: 0.7874 (m-30) cc_final: 0.7540 (t70) REVERT: C 169 TYR cc_start: 0.8430 (m-80) cc_final: 0.8203 (m-80) REVERT: C 374 CYS cc_start: 0.6783 (m) cc_final: 0.6440 (m) REVERT: D 41 GLN cc_start: 0.7202 (pp30) cc_final: 0.6702 (pt0) REVERT: D 157 ASP cc_start: 0.7255 (p0) cc_final: 0.6816 (p0) REVERT: E 176 MET cc_start: 0.7428 (tpt) cc_final: 0.6912 (mmt) REVERT: E 187 ASP cc_start: 0.7906 (m-30) cc_final: 0.7696 (m-30) REVERT: E 217 CYS cc_start: 0.7123 (m) cc_final: 0.6818 (m) REVERT: E 269 MET cc_start: 0.6385 (mtp) cc_final: 0.5901 (mtt) REVERT: F 64 ILE cc_start: 0.8378 (pt) cc_final: 0.8041 (tt) REVERT: F 292 ASP cc_start: 0.7911 (t70) cc_final: 0.7691 (t0) REVERT: F 324 THR cc_start: 0.8665 (p) cc_final: 0.8118 (t) REVERT: G 81 ASP cc_start: 0.8334 (m-30) cc_final: 0.8086 (m-30) REVERT: G 185 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8343 (mm) REVERT: G 239 SER cc_start: 0.7588 (m) cc_final: 0.7376 (p) REVERT: G 313 MET cc_start: 0.8458 (mtp) cc_final: 0.8248 (mtp) outliers start: 33 outliers final: 18 residues processed: 292 average time/residue: 0.3038 time to fit residues: 141.3712 Evaluate side-chains 254 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 266 optimal weight: 0.0010 chunk 83 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 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 = 0.3651 r_free = 0.3651 target = 0.113464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096747 restraints weight = 49490.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098690 restraints weight = 30612.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100026 restraints weight = 22219.241| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21924 Z= 0.130 Angle : 0.600 7.831 29739 Z= 0.295 Chirality : 0.046 0.152 3281 Planarity : 0.004 0.045 3827 Dihedral : 7.269 97.564 3048 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.97 % Allowed : 13.19 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.16), residues: 2691 helix: 0.36 (0.17), residues: 918 sheet: 0.31 (0.24), residues: 484 loop : 0.06 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.018 0.001 PHE A 31 TYR 0.016 0.001 TYR A 111 ARG 0.004 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 907) hydrogen bonds : angle 5.23783 ( 2370) covalent geometry : bond 0.00308 (21924) covalent geometry : angle 0.60034 (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 314 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: B 148 THR cc_start: 0.8331 (m) cc_final: 0.7878 (p) REVERT: B 179 ASP cc_start: 0.7998 (m-30) cc_final: 0.7521 (t70) REVERT: C 169 TYR cc_start: 0.8505 (m-80) cc_final: 0.8274 (m-80) REVERT: D 41 GLN cc_start: 0.7215 (pp30) cc_final: 0.6849 (pt0) REVERT: D 157 ASP cc_start: 0.7134 (p0) cc_final: 0.6788 (p0) REVERT: D 253 GLU cc_start: 0.7918 (mp0) cc_final: 0.7635 (mp0) REVERT: E 269 MET cc_start: 0.6607 (mtp) cc_final: 0.6094 (mtt) REVERT: F 64 ILE cc_start: 0.8478 (pt) cc_final: 0.8127 (tt) REVERT: F 145 SER cc_start: 0.9212 (t) cc_final: 0.8944 (m) REVERT: F 292 ASP cc_start: 0.7910 (t70) cc_final: 0.7646 (t0) REVERT: F 324 THR cc_start: 0.8724 (p) cc_final: 0.8161 (t) REVERT: G 65 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7599 (pp) REVERT: G 82 MET cc_start: 0.8537 (tpt) cc_final: 0.7905 (tpt) REVERT: G 185 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mm) REVERT: G 239 SER cc_start: 0.7756 (m) cc_final: 0.7500 (p) REVERT: G 248 ILE cc_start: 0.8682 (pt) cc_final: 0.8473 (pt) outliers start: 45 outliers final: 22 residues processed: 300 average time/residue: 0.3005 time to fit residues: 144.3095 Evaluate side-chains 267 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 380 LEU 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 180 LEU 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 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 18 LYS 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 60 SER Chi-restraints excluded: chain G residue 65 LEU 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: 0.9980 chunk 46 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093214 restraints weight = 49690.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094099 restraints weight = 32677.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094746 restraints weight = 25398.588| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21924 Z= 0.236 Angle : 0.692 9.146 29739 Z= 0.344 Chirality : 0.049 0.172 3281 Planarity : 0.005 0.045 3827 Dihedral : 7.778 103.271 3048 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.62 % Allowed : 14.50 % Favored : 82.87 % 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: -0.05 (0.16), residues: 2691 helix: 0.25 (0.17), residues: 924 sheet: 0.08 (0.24), residues: 479 loop : -0.13 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 340 HIS 0.006 0.001 HIS C 101 PHE 0.019 0.002 PHE A 31 TYR 0.014 0.002 TYR G 198 ARG 0.005 0.001 ARG G 147 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 907) hydrogen bonds : angle 5.34264 ( 2370) covalent geometry : bond 0.00561 (21924) covalent geometry : angle 0.69188 (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 303 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 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: 0.7601 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: B 179 ASP cc_start: 0.8063 (m-30) cc_final: 0.7638 (t70) REVERT: C 169 TYR cc_start: 0.8609 (m-80) cc_final: 0.8394 (m-80) REVERT: D 157 ASP cc_start: 0.7441 (p0) cc_final: 0.6913 (p0) REVERT: E 176 MET cc_start: 0.7433 (tpt) cc_final: 0.6995 (mmt) REVERT: E 269 MET cc_start: 0.6657 (mtp) cc_final: 0.6129 (mtt) REVERT: F 64 ILE cc_start: 0.8534 (pt) cc_final: 0.8180 (tt) REVERT: F 292 ASP cc_start: 0.7948 (t70) cc_final: 0.7746 (t0) REVERT: F 324 THR cc_start: 0.8779 (p) cc_final: 0.8277 (t) REVERT: G 65 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7733 (pp) REVERT: G 82 MET cc_start: 0.8582 (tpt) cc_final: 0.7979 (tpt) REVERT: G 143 TYR cc_start: 0.7445 (m-80) cc_final: 0.7047 (m-80) REVERT: G 185 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8449 (mm) outliers start: 60 outliers final: 38 residues processed: 287 average time/residue: 0.3110 time to fit residues: 140.8580 Evaluate side-chains 266 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain 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 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 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 C residue 369 ILE 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 6 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 10 CYS Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 65 LEU 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 60 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU 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: 10.0000 chunk 134 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.112829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096210 restraints weight = 48938.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098108 restraints weight = 30492.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099378 restraints weight = 22206.620| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2852 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= 0.118 Angle : 0.598 9.449 29739 Z= 0.293 Chirality : 0.045 0.153 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.392 95.470 3048 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.14 % Allowed : 15.73 % Favored : 82.13 % 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: 0.18 (0.16), residues: 2691 helix: 0.37 (0.18), residues: 924 sheet: 0.25 (0.24), residues: 469 loop : 0.04 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 340 HIS 0.003 0.001 HIS B 371 PHE 0.016 0.001 PHE A 31 TYR 0.016 0.001 TYR G 198 ARG 0.013 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 907) hydrogen bonds : angle 5.10192 ( 2370) covalent geometry : bond 0.00280 (21924) covalent geometry : angle 0.59824 (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 307 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: B 148 THR cc_start: 0.8241 (m) cc_final: 0.7852 (p) REVERT: B 179 ASP cc_start: 0.8046 (m-30) cc_final: 0.7577 (t70) REVERT: B 283 MET cc_start: 0.8376 (tpp) cc_final: 0.7855 (mpp) REVERT: C 169 TYR cc_start: 0.8470 (m-80) cc_final: 0.8237 (m-80) REVERT: C 176 MET cc_start: 0.7989 (mmt) cc_final: 0.7501 (mmt) REVERT: D 157 ASP cc_start: 0.7519 (p0) cc_final: 0.7048 (p0) REVERT: E 192 ILE cc_start: 0.9386 (tp) cc_final: 0.9039 (tp) REVERT: E 269 MET cc_start: 0.6537 (mtp) cc_final: 0.6073 (mtt) REVERT: F 64 ILE cc_start: 0.8339 (pt) cc_final: 0.8048 (tt) REVERT: F 107 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7365 (tm-30) REVERT: F 198 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: F 226 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: F 324 THR cc_start: 0.8671 (p) cc_final: 0.8186 (t) REVERT: G 65 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7627 (pp) REVERT: G 143 TYR cc_start: 0.7230 (m-80) cc_final: 0.6931 (m-80) REVERT: G 185 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 49 outliers final: 23 residues processed: 293 average time/residue: 0.2975 time to fit residues: 140.1989 Evaluate side-chains 271 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 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 C residue 43 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 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 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 265 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU 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: 0.5980 chunk 226 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.111968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095362 restraints weight = 49224.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097175 restraints weight = 30925.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098428 restraints weight = 22692.462| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21924 Z= 0.139 Angle : 0.613 9.946 29739 Z= 0.300 Chirality : 0.046 0.156 3281 Planarity : 0.004 0.045 3827 Dihedral : 7.357 96.687 3048 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.18 % Allowed : 16.56 % Favored : 81.26 % 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: 0.18 (0.16), residues: 2691 helix: 0.40 (0.17), residues: 924 sheet: 0.25 (0.24), residues: 469 loop : 0.02 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 340 HIS 0.004 0.001 HIS E 161 PHE 0.016 0.001 PHE A 31 TYR 0.031 0.001 TYR F 362 ARG 0.010 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 907) hydrogen bonds : angle 4.98274 ( 2370) covalent geometry : bond 0.00332 (21924) covalent geometry : angle 0.61255 (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 298 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: B 148 THR cc_start: 0.8241 (m) cc_final: 0.7786 (p) REVERT: B 179 ASP cc_start: 0.7978 (m-30) cc_final: 0.7616 (t70) REVERT: B 283 MET cc_start: 0.8333 (tpp) cc_final: 0.7828 (mpp) REVERT: C 169 TYR cc_start: 0.8484 (m-80) cc_final: 0.8262 (m-80) REVERT: C 221 LEU cc_start: 0.7741 (mm) cc_final: 0.7494 (mm) REVERT: D 157 ASP cc_start: 0.7341 (p0) cc_final: 0.6902 (p0) REVERT: E 192 ILE cc_start: 0.9373 (tp) cc_final: 0.9069 (tp) REVERT: E 269 MET cc_start: 0.6550 (mtp) cc_final: 0.6094 (mtt) REVERT: F 64 ILE cc_start: 0.8391 (pt) cc_final: 0.8103 (tt) REVERT: F 198 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: F 226 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: F 324 THR cc_start: 0.8696 (p) cc_final: 0.8230 (t) REVERT: G 65 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7737 (pp) REVERT: G 143 TYR cc_start: 0.7314 (m-80) cc_final: 0.6983 (m-80) REVERT: G 185 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8385 (mm) REVERT: G 354 GLN cc_start: 0.7208 (tp40) cc_final: 0.6965 (tp-100) outliers start: 50 outliers final: 32 residues processed: 281 average time/residue: 0.2926 time to fit residues: 132.8934 Evaluate side-chains 267 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 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 A residue 296 LEU Chi-restraints excluded: chain A residue 413 VAL 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 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 369 ILE 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 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 10 CYS Chi-restraints excluded: chain F residue 65 LEU 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 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 283 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 0.0970 chunk 265 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097165 restraints weight = 49075.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099059 restraints weight = 30439.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100347 restraints weight = 22164.911| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3096 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= 0.111 Angle : 0.592 10.391 29739 Z= 0.288 Chirality : 0.045 0.156 3281 Planarity : 0.004 0.044 3827 Dihedral : 7.171 92.842 3048 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.83 % Allowed : 17.21 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.17), residues: 2691 helix: 0.43 (0.18), residues: 924 sheet: 0.27 (0.24), residues: 469 loop : 0.13 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.015 0.001 PHE A 31 TYR 0.024 0.001 TYR F 362 ARG 0.008 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 907) hydrogen bonds : angle 4.93005 ( 2370) covalent geometry : bond 0.00264 (21924) covalent geometry : angle 0.59157 (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 293 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: B 148 THR cc_start: 0.8201 (m) cc_final: 0.7706 (p) REVERT: B 283 MET cc_start: 0.8277 (tpp) cc_final: 0.7820 (mpp) REVERT: C 169 TYR cc_start: 0.8434 (m-80) cc_final: 0.8218 (m-80) REVERT: C 176 MET cc_start: 0.7974 (mmt) cc_final: 0.7435 (mmt) REVERT: C 221 LEU cc_start: 0.7738 (mm) cc_final: 0.7487 (mm) REVERT: D 86 TRP cc_start: 0.8550 (m-10) cc_final: 0.8146 (m-10) REVERT: D 157 ASP cc_start: 0.7440 (p0) cc_final: 0.6983 (p0) REVERT: E 192 ILE cc_start: 0.9411 (tp) cc_final: 0.9105 (tp) REVERT: E 269 MET cc_start: 0.6500 (mtp) cc_final: 0.6033 (mtt) REVERT: F 64 ILE cc_start: 0.8368 (pt) cc_final: 0.8085 (tt) REVERT: F 198 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: F 226 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: F 324 THR cc_start: 0.8685 (p) cc_final: 0.8228 (t) REVERT: G 65 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7607 (pp) REVERT: G 143 TYR cc_start: 0.7278 (m-80) cc_final: 0.6963 (m-80) outliers start: 42 outliers final: 27 residues processed: 278 average time/residue: 0.2881 time to fit residues: 129.6757 Evaluate side-chains 266 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 413 VAL 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 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 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 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 260 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 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: 0.9990 chunk 183 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094684 restraints weight = 49224.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096513 restraints weight = 30891.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097760 restraints weight = 22634.050| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21924 Z= 0.172 Angle : 0.649 10.629 29739 Z= 0.317 Chirality : 0.047 0.164 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.373 97.806 3048 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.01 % Allowed : 17.30 % Favored : 80.69 % 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: 0.16 (0.16), residues: 2691 helix: 0.42 (0.17), residues: 924 sheet: 0.17 (0.24), residues: 469 loop : 0.02 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.014 0.001 PHE A 31 TYR 0.022 0.001 TYR F 362 ARG 0.007 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 907) hydrogen bonds : angle 4.96169 ( 2370) covalent geometry : bond 0.00410 (21924) covalent geometry : angle 0.64876 (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 281 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: B 148 THR cc_start: 0.8181 (m) cc_final: 0.7713 (p) REVERT: B 283 MET cc_start: 0.8334 (tpp) cc_final: 0.7769 (mpp) REVERT: C 149 THR cc_start: 0.8545 (p) cc_final: 0.8204 (t) REVERT: C 169 TYR cc_start: 0.8495 (m-80) cc_final: 0.8258 (m-80) REVERT: C 221 LEU cc_start: 0.7830 (mm) cc_final: 0.7585 (mm) REVERT: D 157 ASP cc_start: 0.7365 (p0) cc_final: 0.6885 (p0) REVERT: E 192 ILE cc_start: 0.9415 (tp) cc_final: 0.9140 (tp) REVERT: E 269 MET cc_start: 0.6553 (mtp) cc_final: 0.6104 (mtt) REVERT: F 64 ILE cc_start: 0.8415 (pt) cc_final: 0.8126 (tt) REVERT: F 198 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: F 226 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: F 324 THR cc_start: 0.8745 (p) cc_final: 0.8318 (t) REVERT: G 65 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7762 (pp) REVERT: G 143 TYR cc_start: 0.7495 (m-80) cc_final: 0.7162 (m-80) outliers start: 46 outliers final: 32 residues processed: 266 average time/residue: 0.3051 time to fit residues: 130.3486 Evaluate side-chains 273 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 413 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 MET 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 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 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 65 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Chi-restraints excluded: chain G residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 173 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 185 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 259 optimal weight: 0.0770 chunk 109 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097456 restraints weight = 48890.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099377 restraints weight = 30258.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100655 restraints weight = 21938.339| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21924 Z= 0.105 Angle : 0.609 11.613 29739 Z= 0.294 Chirality : 0.045 0.160 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.095 90.866 3048 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 17.78 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.17), residues: 2691 helix: 0.51 (0.18), residues: 924 sheet: 0.20 (0.24), residues: 469 loop : 0.16 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.013 0.001 PHE A 31 TYR 0.022 0.001 TYR F 362 ARG 0.007 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 907) hydrogen bonds : angle 4.87059 ( 2370) covalent geometry : bond 0.00243 (21924) covalent geometry : angle 0.60906 (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 295 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: B 148 THR cc_start: 0.8133 (m) cc_final: 0.7661 (p) REVERT: B 283 MET cc_start: 0.8216 (tpp) cc_final: 0.7731 (mpp) REVERT: C 149 THR cc_start: 0.8495 (p) cc_final: 0.8203 (t) REVERT: C 169 TYR cc_start: 0.8415 (m-80) cc_final: 0.8204 (m-80) REVERT: C 176 MET cc_start: 0.7969 (mmt) cc_final: 0.7481 (mmt) REVERT: C 221 LEU cc_start: 0.7792 (mm) cc_final: 0.7527 (mm) REVERT: D 86 TRP cc_start: 0.8544 (m-10) cc_final: 0.8226 (m-10) REVERT: D 157 ASP cc_start: 0.7451 (p0) cc_final: 0.7000 (p0) REVERT: E 192 ILE cc_start: 0.9429 (tp) cc_final: 0.9125 (tp) REVERT: E 269 MET cc_start: 0.6508 (mtp) cc_final: 0.6036 (mtt) REVERT: E 283 MET cc_start: 0.7942 (mmm) cc_final: 0.7453 (mtt) REVERT: F 64 ILE cc_start: 0.8388 (pt) cc_final: 0.8133 (tt) REVERT: F 198 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: F 226 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: F 299 MET cc_start: 0.6882 (mmm) cc_final: 0.6238 (mtt) REVERT: F 324 THR cc_start: 0.8744 (p) cc_final: 0.8360 (t) REVERT: G 65 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7606 (pp) REVERT: G 143 TYR cc_start: 0.7359 (m-80) cc_final: 0.7026 (m-80) outliers start: 36 outliers final: 27 residues processed: 283 average time/residue: 0.3097 time to fit residues: 139.9936 Evaluate side-chains 269 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET 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 180 LEU 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 165 ILE 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 10 CYS Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain G residue 305 MET Chi-restraints excluded: chain G residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 68 optimal weight: 0.5980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097383 restraints weight = 48945.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099272 restraints weight = 30473.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100514 restraints weight = 22216.462| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21924 Z= 0.110 Angle : 0.605 11.484 29739 Z= 0.291 Chirality : 0.045 0.161 3281 Planarity : 0.004 0.045 3827 Dihedral : 6.975 90.313 3048 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.57 % Allowed : 17.91 % 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: 0.39 (0.17), residues: 2691 helix: 0.56 (0.18), residues: 924 sheet: 0.27 (0.24), residues: 469 loop : 0.20 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 340 HIS 0.005 0.001 HIS B 371 PHE 0.012 0.001 PHE A 31 TYR 0.020 0.001 TYR F 362 ARG 0.006 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 907) hydrogen bonds : angle 4.76760 ( 2370) covalent geometry : bond 0.00261 (21924) covalent geometry : angle 0.60485 (29739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6245.65 seconds wall clock time: 110 minutes 49.20 seconds (6649.20 seconds total)