Starting phenix.real_space_refine on Thu Jul 31 20:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572.map" model { file = "/net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2j_20572/07_2025/6q2j_20572_neut.cif" } resolution = 4.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 132 5.16 5 C 8612 2.51 5 N 2426 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1477 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain: "E" Number of atoms: 4493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4493 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 535} Chain breaks: 5 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Restraints were copied for chains: B, F, D Time building chain proxies: 11.49, per 1000 atoms: 0.83 Number of scatterers: 13796 At special positions: 0 Unit cell: (129.47, 172.27, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 132 16.00 O 2618 8.00 N 2426 7.00 C 8612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 305 " distance=2.01 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 307 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 305 " distance=2.01 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 307 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 220 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 233 " distance=2.03 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 304 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.03 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 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 Links applied NAG-ASN " NAG E 701 " - " ASN E 361 " " NAG E 702 " - " ASN E 336 " " NAG E 703 " - " ASN E 377 " " NAG E 704 " - " ASN E 394 " " NAG E 705 " - " ASN E 468 " " NAG E 706 " - " ASN E 367 " " NAG E 707 " - " ASN E 98 " " NAG F 701 " - " ASN F 361 " " NAG F 702 " - " ASN F 336 " " NAG F 703 " - " ASN F 377 " " NAG F 704 " - " ASN F 394 " " NAG F 705 " - " ASN F 468 " " NAG F 706 " - " ASN F 367 " " NAG F 707 " - " ASN F 98 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 23.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.759A pdb=" N GLN A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.657A pdb=" N GLN C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN C 288 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 327' Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.891A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 475 through 478 removed outlier: 3.510A pdb=" N CYS E 478 " --> pdb=" O ARG E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 475 through 478' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.582A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 252 through 265 removed outlier: 3.760A pdb=" N GLN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.658A pdb=" N GLN D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN D 288 " --> pdb=" O THR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN F 327 " --> pdb=" O THR F 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 327' Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.890A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 475 through 478 removed outlier: 3.509A pdb=" N CYS F 478 " --> pdb=" O ARG F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 475 through 478' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.581A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG A 212 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 241 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS A 274 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 307 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A 305 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 278 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET A 282 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP A 299 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 284 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 297 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN A 286 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 295 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 288 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 293 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.293A pdb=" N LEU E 97 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 94 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.954A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE E 174 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR E 263 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 176 " --> pdb=" O TYR E 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL E 223 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU E 222 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 217 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 278 through 283 removed outlier: 3.859A pdb=" N ALA E 279 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 394 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 396 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL E 292 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU E 358 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.155A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB7, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AB9, first strand: chain 'B' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG B 212 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 241 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS B 274 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS B 307 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS B 305 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 278 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 282 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP B 299 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 284 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR B 297 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN B 286 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 295 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 288 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 293 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.292A pdb=" N LEU F 97 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 94 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.953A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE F 174 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR F 263 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 176 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL F 223 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU F 222 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 217 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 278 through 283 removed outlier: 3.858A pdb=" N ALA F 279 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 394 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 396 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL F 292 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 358 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.154A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 594 through 596 424 hydrogen bonds defined for protein. 1176 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: 4.34 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4577 1.34 - 1.47: 3332 1.47 - 1.59: 6031 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 14090 Sorted by residual: bond pdb=" C1 NAG E 707 " pdb=" O5 NAG E 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG F 707 " pdb=" O5 NAG F 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 bond pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 14085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18382 2.19 - 4.37: 647 4.37 - 6.56: 75 6.56 - 8.75: 26 8.75 - 10.94: 10 Bond angle restraints: 19140 Sorted by residual: angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C CYS C 252 " pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.21e+01 angle pdb=" C CYS D 252 " pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 angle pdb=" N ASP E 584 " pdb=" CA ASP E 584 " pdb=" C ASP E 584 " ideal model delta sigma weight residual 114.09 106.53 7.56 1.55e+00 4.16e-01 2.38e+01 ... (remaining 19135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 8472 16.65 - 33.29: 305 33.29 - 49.94: 68 49.94 - 66.59: 8 66.59 - 83.23: 8 Dihedral angle restraints: 8861 sinusoidal: 3789 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.23 83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS E 426 " pdb=" SG CYS E 426 " pdb=" SG CYS E 430 " pdb=" CB CYS E 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.21 83.21 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C 191 " pdb=" SG CYS C 191 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 8858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1984 0.097 - 0.194: 194 0.194 - 0.292: 2 0.292 - 0.389: 0 0.389 - 0.486: 6 Chirality restraints: 2186 Sorted by residual: chirality pdb=" C1 NAG E 706 " pdb=" ND2 ASN E 367 " pdb=" C2 NAG E 706 " pdb=" O5 NAG E 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG F 706 " pdb=" ND2 ASN F 367 " pdb=" C2 NAG F 706 " pdb=" O5 NAG F 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG E 705 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 705 " pdb=" O5 NAG E 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 2183 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 275 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO B 276 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 275 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 276 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 598 " 0.039 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 599 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 599 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 599 " 0.034 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 24 2.32 - 2.97: 6014 2.97 - 3.61: 18089 3.61 - 4.26: 29216 4.26 - 4.90: 48607 Nonbonded interactions: 101950 Sorted by model distance: nonbonded pdb=" OD1 ASP E 230 " pdb=" OE1 GLU E 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 230 " pdb=" OE1 GLU F 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 567 " pdb=" OD2 ASP F 584 " model vdw 1.917 3.040 nonbonded pdb=" OD1 ASP E 567 " pdb=" OD2 ASP E 584 " model vdw 1.918 3.040 nonbonded pdb=" O HIS F 569 " pdb=" OD2 ASP F 584 " model vdw 2.111 3.040 ... (remaining 101945 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.840 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14159 Z= 0.273 Angle : 1.014 12.448 19292 Z= 0.560 Chirality : 0.059 0.486 2186 Planarity : 0.007 0.061 2478 Dihedral : 9.003 70.338 5396 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 0.13 % Allowed : 1.70 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -3.22 (0.18), residues: 1706 helix: -2.97 (0.19), residues: 346 sheet: -1.09 (0.24), residues: 436 loop : -2.35 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP E 334 HIS 0.006 0.001 HIS D 253 PHE 0.025 0.003 PHE F 258 TYR 0.032 0.003 TYR E 263 ARG 0.008 0.001 ARG F 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00982 ( 14) link_NAG-ASN : angle 5.57578 ( 42) hydrogen bonds : bond 0.15524 ( 424) hydrogen bonds : angle 7.39444 ( 1176) SS BOND : bond 0.00519 ( 55) SS BOND : angle 1.43915 ( 110) covalent geometry : bond 0.00581 (14090) covalent geometry : angle 0.97772 (19140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 299 SER cc_start: 0.7256 (p) cc_final: 0.5982 (t) REVERT: D 310 MET cc_start: -0.0991 (mtm) cc_final: -0.2766 (mmp) REVERT: F 255 MET cc_start: -0.2474 (ptp) cc_final: -0.4322 (mtm) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.3136 time to fit residues: 139.3920 Evaluate side-chains 139 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 286 GLN C 184 GLN C 200 GLN C 228 GLN E 84 ASN E 333 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 ASN B 236 GLN B 286 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 594 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.190918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.169019 restraints weight = 42303.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.170456 restraints weight = 29208.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.172434 restraints weight = 20888.304| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4475 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 14159 Z= 0.253 Angle : 0.877 10.741 19292 Z= 0.448 Chirality : 0.053 0.403 2186 Planarity : 0.007 0.070 2478 Dihedral : 7.037 59.978 2182 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.71 (0.19), residues: 1706 helix: -2.16 (0.22), residues: 372 sheet: -1.20 (0.23), residues: 496 loop : -1.94 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 334 HIS 0.018 0.002 HIS B 254 PHE 0.022 0.003 PHE F 31 TYR 0.032 0.003 TYR B 297 ARG 0.012 0.001 ARG E 144 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 14) link_NAG-ASN : angle 4.09475 ( 42) hydrogen bonds : bond 0.05049 ( 424) hydrogen bonds : angle 6.40063 ( 1176) SS BOND : bond 0.01114 ( 55) SS BOND : angle 1.56264 ( 110) covalent geometry : bond 0.00530 (14090) covalent geometry : angle 0.85087 (19140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.2634 (mt) cc_final: 0.1769 (pt) REVERT: C 185 MET cc_start: 0.6586 (mtp) cc_final: 0.5854 (mmm) REVERT: C 196 ILE cc_start: 0.8136 (tp) cc_final: 0.7856 (pt) REVERT: C 299 SER cc_start: 0.8204 (p) cc_final: 0.7391 (m) REVERT: E 43 ASP cc_start: 0.7172 (t70) cc_final: 0.6947 (t0) REVERT: E 486 VAL cc_start: 0.6248 (t) cc_final: 0.5190 (t) REVERT: E 497 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6657 (mm-40) REVERT: B 253 MET cc_start: 0.6435 (ptm) cc_final: 0.5877 (ptp) REVERT: D 310 MET cc_start: -0.0080 (mtm) cc_final: -0.1491 (mmp) REVERT: F 255 MET cc_start: -0.3619 (ptp) cc_final: -0.5208 (mtt) outliers start: 3 outliers final: 2 residues processed: 212 average time/residue: 0.2646 time to fit residues: 81.4024 Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 443 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN D 236 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.189875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.170262 restraints weight = 42886.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.171949 restraints weight = 35578.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.173017 restraints weight = 25002.150| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14159 Z= 0.143 Angle : 0.694 12.467 19292 Z= 0.347 Chirality : 0.049 0.372 2186 Planarity : 0.006 0.068 2478 Dihedral : 6.196 53.923 2182 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.12 (0.19), residues: 1706 helix: -1.21 (0.25), residues: 350 sheet: -0.96 (0.23), residues: 480 loop : -1.70 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 139 HIS 0.010 0.001 HIS D 236 PHE 0.017 0.002 PHE C 307 TYR 0.020 0.002 TYR E 354 ARG 0.011 0.001 ARG E 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00998 ( 14) link_NAG-ASN : angle 3.89035 ( 42) hydrogen bonds : bond 0.03966 ( 424) hydrogen bonds : angle 5.95558 ( 1176) SS BOND : bond 0.00303 ( 55) SS BOND : angle 1.59438 ( 110) covalent geometry : bond 0.00315 (14090) covalent geometry : angle 0.66129 (19140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.6126 (mtp) cc_final: 0.5628 (mmm) REVERT: C 254 GLU cc_start: 0.3893 (OUTLIER) cc_final: 0.3483 (mp0) REVERT: C 299 SER cc_start: 0.8035 (p) cc_final: 0.7164 (m) REVERT: E 43 ASP cc_start: 0.7019 (t70) cc_final: 0.6771 (t0) REVERT: E 408 TYR cc_start: 0.4733 (m-80) cc_final: 0.4456 (m-80) REVERT: E 486 VAL cc_start: 0.6628 (t) cc_final: 0.5452 (t) REVERT: B 253 MET cc_start: 0.7073 (ptm) cc_final: 0.6626 (ptm) REVERT: B 279 TYR cc_start: 0.5688 (m-80) cc_final: 0.5343 (m-80) REVERT: D 168 GLN cc_start: 0.3458 (mm110) cc_final: 0.3247 (mm110) REVERT: D 310 MET cc_start: 0.0476 (mtm) cc_final: -0.1012 (mmp) REVERT: F 255 MET cc_start: -0.3348 (ptp) cc_final: -0.5100 (mtt) REVERT: F 473 LEU cc_start: 0.4227 (tp) cc_final: 0.3328 (tp) REVERT: F 579 ASN cc_start: 0.6237 (p0) cc_final: 0.5945 (m-40) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2723 time to fit residues: 76.3448 Evaluate side-chains 128 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 105 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN E 495 GLN E 497 GLN B 254 HIS D 184 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS F 429 ASN F 583 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.175859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.156175 restraints weight = 41898.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.156158 restraints weight = 42166.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.157895 restraints weight = 35553.939| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.164 14159 Z= 0.308 Angle : 1.011 13.423 19292 Z= 0.520 Chirality : 0.057 0.381 2186 Planarity : 0.008 0.141 2478 Dihedral : 7.331 46.858 2182 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.97 % Favored : 90.97 % Rotamer: Outliers : 0.39 % Allowed : 4.57 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.59 (0.19), residues: 1706 helix: -2.12 (0.25), residues: 347 sheet: -1.13 (0.24), residues: 441 loop : -1.84 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP E 334 HIS 0.015 0.003 HIS C 236 PHE 0.061 0.003 PHE D 188 TYR 0.049 0.004 TYR D 279 ARG 0.017 0.001 ARG F 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 14) link_NAG-ASN : angle 3.79088 ( 42) hydrogen bonds : bond 0.05559 ( 424) hydrogen bonds : angle 7.48936 ( 1176) SS BOND : bond 0.01186 ( 55) SS BOND : angle 2.55189 ( 110) covalent geometry : bond 0.00677 (14090) covalent geometry : angle 0.98058 (19140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8103 (m) REVERT: C 185 MET cc_start: 0.6853 (mtp) cc_final: 0.6525 (mmm) REVERT: C 186 LEU cc_start: 0.8208 (tt) cc_final: 0.7994 (tp) REVERT: C 256 GLU cc_start: 0.7853 (pm20) cc_final: 0.7644 (mp0) REVERT: C 296 ILE cc_start: 0.8658 (pt) cc_final: 0.8206 (pt) REVERT: C 301 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6243 (tp30) REVERT: C 305 LYS cc_start: 0.7478 (mtpt) cc_final: 0.7159 (mtmt) REVERT: C 307 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: E 39 LYS cc_start: 0.6236 (mttt) cc_final: 0.6035 (mmtt) REVERT: B 252 ASN cc_start: 0.8526 (p0) cc_final: 0.7555 (m-40) REVERT: B 253 MET cc_start: 0.7768 (ptm) cc_final: 0.7514 (ptm) REVERT: D 175 TYR cc_start: 0.4531 (m-10) cc_final: 0.4312 (m-80) REVERT: D 310 MET cc_start: 0.2686 (mtm) cc_final: 0.1292 (mmp) REVERT: F 255 MET cc_start: -0.3518 (ptp) cc_final: -0.4123 (mtt) REVERT: F 370 MET cc_start: 0.0316 (mpp) cc_final: -0.1599 (tpt) REVERT: F 523 LYS cc_start: 0.7685 (ptmt) cc_final: 0.7145 (pttp) outliers start: 6 outliers final: 1 residues processed: 220 average time/residue: 0.2551 time to fit residues: 81.7379 Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN E 392 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.179928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.160719 restraints weight = 41848.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.161844 restraints weight = 37347.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.163179 restraints weight = 27182.710| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.8957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14159 Z= 0.135 Angle : 0.747 20.201 19292 Z= 0.372 Chirality : 0.049 0.347 2186 Planarity : 0.006 0.106 2478 Dihedral : 6.021 43.418 2182 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.21 (0.19), residues: 1706 helix: -1.61 (0.25), residues: 368 sheet: -0.85 (0.25), residues: 424 loop : -1.68 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 334 HIS 0.008 0.001 HIS D 253 PHE 0.033 0.002 PHE D 173 TYR 0.017 0.001 TYR E 122 ARG 0.006 0.001 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 14) link_NAG-ASN : angle 3.33111 ( 42) hydrogen bonds : bond 0.03876 ( 424) hydrogen bonds : angle 6.38212 ( 1176) SS BOND : bond 0.00496 ( 55) SS BOND : angle 1.81172 ( 110) covalent geometry : bond 0.00299 (14090) covalent geometry : angle 0.72009 (19140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7289 (mtmt) REVERT: E 39 LYS cc_start: 0.6225 (mttt) cc_final: 0.5700 (mmtt) REVERT: E 94 LEU cc_start: 0.8712 (tp) cc_final: 0.8503 (tp) REVERT: B 252 ASN cc_start: 0.8437 (p0) cc_final: 0.7777 (m110) REVERT: D 168 GLN cc_start: 0.5459 (mm110) cc_final: 0.5218 (mm110) REVERT: D 310 MET cc_start: 0.2354 (mtm) cc_final: 0.2031 (mtm) REVERT: F 237 TYR cc_start: 0.2483 (m-80) cc_final: 0.1997 (m-80) REVERT: F 255 MET cc_start: -0.3803 (ptp) cc_final: -0.4816 (mtt) REVERT: F 422 ILE cc_start: 0.4849 (mp) cc_final: 0.4380 (mm) REVERT: F 523 LYS cc_start: 0.7497 (ptmt) cc_final: 0.7005 (pttp) REVERT: F 595 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7073 (tm-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2435 time to fit residues: 71.2793 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 147 optimal weight: 30.0000 chunk 120 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN E 579 ASN D 228 GLN D 236 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.176869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.157920 restraints weight = 42241.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.159306 restraints weight = 43423.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.159696 restraints weight = 36562.086| |-----------------------------------------------------------------------------| r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.9488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 14159 Z= 0.154 Angle : 0.764 18.229 19292 Z= 0.377 Chirality : 0.050 0.334 2186 Planarity : 0.005 0.080 2478 Dihedral : 5.694 40.892 2182 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.04 (0.19), residues: 1706 helix: -1.34 (0.25), residues: 368 sheet: -0.85 (0.24), residues: 442 loop : -1.58 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 228 HIS 0.006 0.001 HIS D 253 PHE 0.024 0.002 PHE E 612 TYR 0.016 0.002 TYR E 146 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 14) link_NAG-ASN : angle 3.21886 ( 42) hydrogen bonds : bond 0.03850 ( 424) hydrogen bonds : angle 6.28763 ( 1176) SS BOND : bond 0.00652 ( 55) SS BOND : angle 1.99194 ( 110) covalent geometry : bond 0.00355 (14090) covalent geometry : angle 0.73649 (19140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.6253 (tt) cc_final: 0.5775 (mt) REVERT: C 185 MET cc_start: 0.7021 (mtp) cc_final: 0.6418 (mmm) REVERT: C 214 MET cc_start: 0.7690 (mmp) cc_final: 0.7067 (mtp) REVERT: C 281 ASP cc_start: 0.7823 (t0) cc_final: 0.7561 (p0) REVERT: C 301 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6571 (tp30) REVERT: C 305 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7406 (mtmt) REVERT: E 39 LYS cc_start: 0.6595 (mttt) cc_final: 0.6162 (mmtt) REVERT: E 606 TYR cc_start: 0.5908 (t80) cc_final: 0.5678 (t80) REVERT: B 288 THR cc_start: 0.5826 (p) cc_final: 0.5492 (p) REVERT: B 299 ASP cc_start: 0.7791 (p0) cc_final: 0.7468 (p0) REVERT: D 310 MET cc_start: 0.3131 (mtm) cc_final: 0.1668 (mmp) REVERT: F 255 MET cc_start: -0.3539 (ptp) cc_final: -0.3918 (mtt) REVERT: F 523 LYS cc_start: 0.7745 (ptmt) cc_final: 0.7229 (tttt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2599 time to fit residues: 75.2210 Evaluate side-chains 134 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS D 236 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 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 = 0.4740 r_free = 0.4740 target = 0.174168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.154134 restraints weight = 41457.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.153979 restraints weight = 44582.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.155195 restraints weight = 40009.289| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 1.0218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 14159 Z= 0.170 Angle : 0.776 19.867 19292 Z= 0.385 Chirality : 0.050 0.360 2186 Planarity : 0.005 0.072 2478 Dihedral : 5.616 41.823 2182 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.90 (0.20), residues: 1706 helix: -1.19 (0.26), residues: 358 sheet: -0.75 (0.25), residues: 440 loop : -1.52 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 228 HIS 0.015 0.002 HIS B 306 PHE 0.024 0.002 PHE C 307 TYR 0.032 0.002 TYR F 36 ARG 0.015 0.001 ARG F 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 14) link_NAG-ASN : angle 3.17101 ( 42) hydrogen bonds : bond 0.03709 ( 424) hydrogen bonds : angle 6.23084 ( 1176) SS BOND : bond 0.00618 ( 55) SS BOND : angle 2.11463 ( 110) covalent geometry : bond 0.00393 (14090) covalent geometry : angle 0.74824 (19140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7116 (m-30) cc_final: 0.6724 (t70) REVERT: C 185 MET cc_start: 0.7101 (mtp) cc_final: 0.6762 (mmm) REVERT: C 214 MET cc_start: 0.7646 (mmp) cc_final: 0.7029 (mtp) REVERT: C 305 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7386 (mtmt) REVERT: E 39 LYS cc_start: 0.6670 (mttt) cc_final: 0.6175 (mmtt) REVERT: B 299 ASP cc_start: 0.7882 (p0) cc_final: 0.7628 (p0) REVERT: D 310 MET cc_start: 0.3108 (mtm) cc_final: 0.1822 (mmp) REVERT: F 237 TYR cc_start: 0.2861 (m-80) cc_final: 0.2411 (m-80) REVERT: F 255 MET cc_start: -0.3778 (ptp) cc_final: -0.4283 (mtm) REVERT: F 422 ILE cc_start: 0.5035 (mp) cc_final: 0.4584 (mm) REVERT: F 523 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7512 (tttt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2386 time to fit residues: 66.0623 Evaluate side-chains 139 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 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 = 0.4759 r_free = 0.4759 target = 0.175541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.156440 restraints weight = 41215.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.157268 restraints weight = 40560.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.158135 restraints weight = 36651.365| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 1.0426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14159 Z= 0.130 Angle : 0.725 18.813 19292 Z= 0.355 Chirality : 0.048 0.312 2186 Planarity : 0.005 0.067 2478 Dihedral : 5.309 39.549 2182 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.69 (0.20), residues: 1706 helix: -0.87 (0.28), residues: 344 sheet: -0.69 (0.25), residues: 438 loop : -1.40 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 228 HIS 0.007 0.001 HIS D 253 PHE 0.026 0.001 PHE D 173 TYR 0.020 0.001 TYR F 36 ARG 0.010 0.000 ARG F 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 14) link_NAG-ASN : angle 3.01323 ( 42) hydrogen bonds : bond 0.03417 ( 424) hydrogen bonds : angle 5.93183 ( 1176) SS BOND : bond 0.00514 ( 55) SS BOND : angle 1.77599 ( 110) covalent geometry : bond 0.00305 (14090) covalent geometry : angle 0.70172 (19140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.6962 (m-30) cc_final: 0.6585 (t70) REVERT: C 185 MET cc_start: 0.7041 (mtp) cc_final: 0.6738 (mmm) REVERT: C 214 MET cc_start: 0.7560 (mmp) cc_final: 0.6979 (mtp) REVERT: C 261 THR cc_start: 0.8697 (p) cc_final: 0.8063 (t) REVERT: C 301 GLU cc_start: 0.6750 (tp30) cc_final: 0.6444 (tp30) REVERT: C 305 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7406 (mtmt) REVERT: E 240 VAL cc_start: 0.6870 (t) cc_final: 0.6655 (t) REVERT: B 299 ASP cc_start: 0.7717 (p0) cc_final: 0.7278 (p0) REVERT: D 310 MET cc_start: 0.3370 (mtm) cc_final: 0.2124 (mmp) REVERT: F 237 TYR cc_start: 0.2703 (m-80) cc_final: 0.2288 (m-80) REVERT: F 422 ILE cc_start: 0.5009 (mp) cc_final: 0.4649 (mm) REVERT: F 523 LYS cc_start: 0.7849 (ptmt) cc_final: 0.7593 (tttt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2562 time to fit residues: 70.4637 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 131 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.172934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.152792 restraints weight = 41172.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.152430 restraints weight = 46516.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.153748 restraints weight = 39439.150| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 1.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14159 Z= 0.147 Angle : 0.746 18.382 19292 Z= 0.369 Chirality : 0.049 0.315 2186 Planarity : 0.005 0.058 2478 Dihedral : 5.291 38.792 2182 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.63 (0.20), residues: 1706 helix: -0.88 (0.27), residues: 356 sheet: -0.64 (0.25), residues: 444 loop : -1.35 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 228 HIS 0.009 0.001 HIS F 569 PHE 0.029 0.002 PHE C 307 TYR 0.020 0.002 TYR F 36 ARG 0.004 0.000 ARG F 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 14) link_NAG-ASN : angle 2.95459 ( 42) hydrogen bonds : bond 0.03501 ( 424) hydrogen bonds : angle 6.03012 ( 1176) SS BOND : bond 0.00511 ( 55) SS BOND : angle 2.06656 ( 110) covalent geometry : bond 0.00342 (14090) covalent geometry : angle 0.71879 (19140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.7820 (t80) cc_final: 0.7614 (t80) REVERT: C 133 GLU cc_start: 0.8532 (tp30) cc_final: 0.8286 (tp30) REVERT: C 214 MET cc_start: 0.7555 (mmp) cc_final: 0.7055 (mtp) REVERT: C 261 THR cc_start: 0.8673 (p) cc_final: 0.8025 (t) REVERT: C 305 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7552 (mtmt) REVERT: B 299 ASP cc_start: 0.7766 (p0) cc_final: 0.7460 (p0) REVERT: D 310 MET cc_start: 0.3585 (mtm) cc_final: 0.2426 (mmp) REVERT: F 73 TYR cc_start: 0.7893 (m-80) cc_final: 0.7634 (m-80) REVERT: F 237 TYR cc_start: 0.2888 (m-80) cc_final: 0.2512 (m-80) REVERT: F 370 MET cc_start: -0.1189 (tpp) cc_final: -0.1637 (tpp) REVERT: F 422 ILE cc_start: 0.5183 (mp) cc_final: 0.4863 (mm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2524 time to fit residues: 68.2831 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 253 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.169980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.148268 restraints weight = 41304.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.149454 restraints weight = 42055.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.150677 restraints weight = 35963.092| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 1.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14159 Z= 0.170 Angle : 0.776 17.825 19292 Z= 0.385 Chirality : 0.049 0.301 2186 Planarity : 0.005 0.059 2478 Dihedral : 5.411 39.791 2182 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.67 (0.20), residues: 1706 helix: -0.87 (0.27), residues: 348 sheet: -0.68 (0.25), residues: 450 loop : -1.39 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 228 HIS 0.008 0.001 HIS E 594 PHE 0.027 0.002 PHE C 307 TYR 0.022 0.002 TYR F 36 ARG 0.007 0.001 ARG F 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 14) link_NAG-ASN : angle 2.91891 ( 42) hydrogen bonds : bond 0.03643 ( 424) hydrogen bonds : angle 6.15052 ( 1176) SS BOND : bond 0.00552 ( 55) SS BOND : angle 2.04036 ( 110) covalent geometry : bond 0.00392 (14090) covalent geometry : angle 0.75151 (19140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.6549 (mp) cc_final: 0.6327 (mp) REVERT: C 133 GLU cc_start: 0.8465 (tp30) cc_final: 0.8239 (tp30) REVERT: C 136 GLU cc_start: 0.7147 (tp30) cc_final: 0.6886 (mm-30) REVERT: C 185 MET cc_start: 0.7096 (mmm) cc_final: 0.6786 (mmm) REVERT: C 208 LYS cc_start: 0.8161 (mppt) cc_final: 0.7223 (mtpt) REVERT: C 214 MET cc_start: 0.7473 (mmp) cc_final: 0.7044 (mtp) REVERT: C 261 THR cc_start: 0.8753 (p) cc_final: 0.8148 (t) REVERT: C 305 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7545 (mtmt) REVERT: B 253 MET cc_start: 0.8887 (ptm) cc_final: 0.8591 (ptm) REVERT: B 299 ASP cc_start: 0.7741 (p0) cc_final: 0.7458 (p0) REVERT: D 310 MET cc_start: 0.3923 (mtm) cc_final: 0.3178 (mmp) REVERT: F 73 TYR cc_start: 0.7953 (m-80) cc_final: 0.7689 (m-80) REVERT: F 237 TYR cc_start: 0.3315 (m-80) cc_final: 0.2924 (m-80) REVERT: F 370 MET cc_start: -0.0790 (tpp) cc_final: -0.1160 (tpp) REVERT: F 523 LYS cc_start: 0.7149 (tttt) cc_final: 0.6894 (mtpt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2504 time to fit residues: 66.4494 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN D 166 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 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 = 0.4722 r_free = 0.4722 target = 0.171972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.151474 restraints weight = 41884.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.150928 restraints weight = 48021.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.152435 restraints weight = 38477.163| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 1.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14159 Z= 0.128 Angle : 0.720 17.507 19292 Z= 0.355 Chirality : 0.048 0.291 2186 Planarity : 0.005 0.059 2478 Dihedral : 5.186 38.296 2182 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.60 (0.20), residues: 1706 helix: -0.85 (0.27), residues: 356 sheet: -0.64 (0.25), residues: 452 loop : -1.34 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 228 HIS 0.009 0.001 HIS D 253 PHE 0.030 0.002 PHE C 307 TYR 0.025 0.001 TYR F 36 ARG 0.007 0.000 ARG F 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 14) link_NAG-ASN : angle 2.80517 ( 42) hydrogen bonds : bond 0.03372 ( 424) hydrogen bonds : angle 5.88302 ( 1176) SS BOND : bond 0.00465 ( 55) SS BOND : angle 1.78894 ( 110) covalent geometry : bond 0.00298 (14090) covalent geometry : angle 0.69804 (19140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.74 seconds wall clock time: 70 minutes 57.72 seconds (4257.72 seconds total)