Starting phenix.real_space_refine on Thu Mar 5 03:34:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.cif Found real_map, /net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.map" model { file = "/net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6njo_9390/03_2026/6njo_9390.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 12092 2.51 5 N 3282 2.21 5 O 3610 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19090 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3176 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3110 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 5.05, per 1000 atoms: 0.26 Number of scatterers: 19090 At special positions: 0 Unit cell: (106.08, 118.32, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 78 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3610 8.00 N 3282 7.00 C 12092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 929.2 milliseconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 20 sheets defined 39.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 236 through 257 removed outlier: 4.371A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.049A pdb=" N PHE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 373 through 398 removed outlier: 3.862A pdb=" N CYS A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.847A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 111' Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.237A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 238 through 257 removed outlier: 5.175A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 282 removed outlier: 4.103A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 removed outlier: 4.086A pdb=" N PHE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.920A pdb=" N VAL B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 392 Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.696A pdb=" N ILE B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 421 removed outlier: 5.186A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.683A pdb=" N LEU C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 111 " --> pdb=" O ASP C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.922A pdb=" N ARG C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 209 through 214 removed outlier: 4.122A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.715A pdb=" N GLN C 257 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 282 removed outlier: 4.085A pdb=" N TYR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.982A pdb=" N PHE C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.618A pdb=" N ALA C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 373 through 399 removed outlier: 5.826A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.733A pdb=" N THR C 437 " --> pdb=" O SER C 433 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 4.030A pdb=" N LEU D 110 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 111 " --> pdb=" O ASP D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 209 through 218 removed outlier: 4.072A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 218 " --> pdb=" O PHE D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 236 through 257 removed outlier: 5.463A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 Processing helix chain 'D' and resid 292 through 299 removed outlier: 4.048A pdb=" N PHE D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.793A pdb=" N VAL D 372 " --> pdb=" O MET D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 394 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.908A pdb=" N ASP D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.861A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.505A pdb=" N ILE D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.613A pdb=" N GLY E 193 " --> pdb=" O MET E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 236 through 257 removed outlier: 5.259A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 281 removed outlier: 3.830A pdb=" N TYR E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 303 removed outlier: 4.157A pdb=" N PHE E 296 " --> pdb=" O PRO E 292 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 373 through 394 removed outlier: 3.955A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 407 through 416 removed outlier: 3.848A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 425 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.688A pdb=" N LEU F 110 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 111 " --> pdb=" O ASP F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 111' Processing helix chain 'F' and resid 143 through 147 removed outlier: 3.849A pdb=" N ARG F 147 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 165 Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.862A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 238 through 257 removed outlier: 5.292A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 257 " --> pdb=" O TYR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.564A pdb=" N TYR F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 331 through 337 Processing helix chain 'F' and resid 348 through 352 removed outlier: 3.785A pdb=" N GLU F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 390 through 399 removed outlier: 4.186A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 416 Processing helix chain 'F' and resid 417 through 424 Processing helix chain 'F' and resid 433 through 443 removed outlier: 3.554A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.791A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE A 79 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 71 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 7.474A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 198 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET A 264 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 200 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 266 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 202 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 317 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 263 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR A 319 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET A 265 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU A 321 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.770A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 79 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.057A pdb=" N ILE B 115 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR B 232 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 199 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL B 229 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 201 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 231 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 203 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 198 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 154 removed outlier: 4.509A pdb=" N CYS B 167 " --> pdb=" O PHE B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 74 removed outlier: 4.283A pdb=" N PHE C 58 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 36 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 73 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE C 79 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE D 58 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE D 41 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS D 47 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.548A pdb=" N ILE C 198 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET C 264 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 200 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE C 317 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU C 263 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR C 319 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET C 265 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LEU C 321 " --> pdb=" O MET C 265 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 173 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL C 320 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 175 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG C 172 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ILE C 343 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 174 " --> pdb=" O ILE C 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.323A pdb=" N CYS C 167 " --> pdb=" O PHE C 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AB4, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.566A pdb=" N LEU D 228 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 199 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL D 229 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 201 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR D 231 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 203 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 198 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 204 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 173 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL D 320 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 175 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 172 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE D 343 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY D 174 " --> pdb=" O ILE D 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.789A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN E 93 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 36 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 103 through 106 Processing sheet with id=AB7, first strand: chain 'E' and resid 114 through 115 removed outlier: 6.700A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 114 through 115 removed outlier: 6.700A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE E 173 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL E 320 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE E 175 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ILE E 343 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY E 174 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 37 through 41 removed outlier: 4.000A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU F 77 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE F 73 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE F 79 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 106 removed outlier: 3.760A pdb=" N PHE F 133 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 114 through 115 removed outlier: 3.565A pdb=" N ILE F 115 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE F 199 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL F 229 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU F 201 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY F 174 " --> pdb=" O ILE F 343 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU F 345 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE F 176 " --> pdb=" O LEU F 345 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5278 1.33 - 1.45: 3114 1.45 - 1.57: 10846 1.57 - 1.69: 20 1.69 - 1.82: 130 Bond restraints: 19388 Sorted by residual: bond pdb=" F3 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" F3 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.732 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" F3 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.731 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" F3 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.730 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CB THR C 269 " pdb=" CG2 THR C 269 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.18e+00 ... (remaining 19383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 25636 3.24 - 6.49: 513 6.49 - 9.73: 93 9.73 - 12.98: 12 12.98 - 16.22: 2 Bond angle restraints: 26256 Sorted by residual: angle pdb=" N ARG E 207 " pdb=" CA ARG E 207 " pdb=" C ARG E 207 " ideal model delta sigma weight residual 110.10 117.79 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C2' ADP C 600 " pdb=" C3' ADP C 600 " pdb=" C4' ADP C 600 " ideal model delta sigma weight residual 111.00 97.09 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LEU E 339 " pdb=" CB LEU E 339 " pdb=" CG LEU E 339 " ideal model delta sigma weight residual 116.30 132.52 -16.22 3.50e+00 8.16e-02 2.15e+01 ... (remaining 26251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 11640 30.27 - 60.53: 173 60.53 - 90.80: 18 90.80 - 121.06: 2 121.06 - 151.33: 2 Dihedral angle restraints: 11835 sinusoidal: 4797 harmonic: 7038 Sorted by residual: dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 148.67 151.33 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP B 600 " pdb=" O5' ADP B 600 " pdb=" PA ADP B 600 " pdb=" O2A ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 175.76 124.25 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" CA TYR A 90 " pdb=" C TYR A 90 " pdb=" N CYS A 91 " pdb=" CA CYS A 91 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 11832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2743 0.111 - 0.222: 277 0.222 - 0.332: 14 0.332 - 0.443: 4 0.443 - 0.554: 1 Chirality restraints: 3039 Sorted by residual: chirality pdb=" CB ILE F 199 " pdb=" CA ILE F 199 " pdb=" CG1 ILE F 199 " pdb=" CG2 ILE F 199 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CB ILE B 314 " pdb=" CA ILE B 314 " pdb=" CG1 ILE B 314 " pdb=" CG2 ILE B 314 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3036 not shown) Planarity restraints: 3388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO C 132 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO D 330 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 425 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" CD GLN B 425 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 425 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 425 " 0.014 2.00e-02 2.50e+03 ... (remaining 3385 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 3959 2.78 - 3.48: 24820 3.48 - 4.19: 44489 4.19 - 4.90: 80351 Nonbonded interactions: 153626 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.361 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.720 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.921 2.170 nonbonded pdb=" NH1 ARG D 366 " pdb=" NH2 ARG E 207 " model vdw 1.929 3.200 nonbonded pdb=" OD1 ASP D 266 " pdb=" O HOH D1002 " model vdw 1.956 3.040 ... (remaining 153621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'D' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'E' and (resid 35 through 322 or resid 330 through 446)) selection = chain 'F' } 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.390 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.010 0.250 19392 Z= 0.464 Angle : 1.199 16.220 26256 Z= 0.609 Chirality : 0.069 0.554 3039 Planarity : 0.008 0.072 3388 Dihedral : 11.616 151.327 7323 Min Nonbonded Distance : 1.361 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.49 % Allowed : 5.54 % Favored : 93.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.13), residues: 2452 helix: -3.09 (0.12), residues: 919 sheet: -2.26 (0.22), residues: 440 loop : -2.72 (0.15), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG E 209 TYR 0.030 0.004 TYR B 434 PHE 0.038 0.004 PHE C 58 TRP 0.010 0.002 TRP B 94 HIS 0.010 0.003 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00983 (19388) covalent geometry : angle 1.19905 (26256) hydrogen bonds : bond 0.17333 ( 715) hydrogen bonds : angle 7.66074 ( 2109) Misc. bond : bond 0.17127 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 315 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6622 (ttm-80) REVERT: A 69 GLU cc_start: 0.4942 (tt0) cc_final: 0.4647 (tp30) REVERT: A 113 ARG cc_start: 0.6918 (mmt-90) cc_final: 0.6529 (mmt90) REVERT: A 267 SER cc_start: 0.8294 (t) cc_final: 0.8039 (p) REVERT: A 436 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7305 (ttpt) REVERT: A 441 LEU cc_start: 0.7067 (tp) cc_final: 0.6813 (tp) REVERT: B 98 GLN cc_start: 0.7839 (mm110) cc_final: 0.7524 (mm110) REVERT: B 368 MET cc_start: 0.8904 (tpt) cc_final: 0.8615 (tpt) REVERT: B 414 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6537 (mp) REVERT: C 41 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 54 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7473 (mpp80) REVERT: C 84 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 220 GLN cc_start: 0.6746 (tp40) cc_final: 0.6160 (tp-100) REVERT: C 398 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.6825 (ttm170) REVERT: C 402 TYR cc_start: 0.6403 (t80) cc_final: 0.6120 (t80) REVERT: D 311 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8159 (mtmm) REVERT: D 436 LYS cc_start: 0.7277 (tmtt) cc_final: 0.6780 (ttpt) REVERT: E 75 GLU cc_start: 0.4953 (tm-30) cc_final: 0.4226 (pp20) REVERT: E 113 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7460 (mmp80) REVERT: E 149 VAL cc_start: 0.7794 (t) cc_final: 0.7489 (p) REVERT: E 271 TYR cc_start: 0.9015 (t80) cc_final: 0.8665 (t80) REVERT: E 311 LYS cc_start: 0.7553 (tptm) cc_final: 0.7230 (ptmt) REVERT: E 431 ILE cc_start: 0.8247 (pt) cc_final: 0.7788 (mm) REVERT: F 52 LYS cc_start: 0.6594 (pttp) cc_final: 0.6297 (tptt) REVERT: F 116 ASP cc_start: 0.7924 (t70) cc_final: 0.7554 (t0) REVERT: F 265 MET cc_start: 0.7606 (ttm) cc_final: 0.7380 (ttm) REVERT: F 394 GLU cc_start: 0.5836 (tp30) cc_final: 0.5570 (tp30) REVERT: F 443 LYS cc_start: 0.6857 (pmtt) cc_final: 0.6532 (mppt) outliers start: 10 outliers final: 3 residues processed: 325 average time/residue: 0.1755 time to fit residues: 80.9544 Evaluate side-chains 225 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 220 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129820 restraints weight = 25016.960| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.65 r_work: 0.3260 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19392 Z= 0.109 Angle : 0.642 7.861 26256 Z= 0.314 Chirality : 0.045 0.205 3039 Planarity : 0.006 0.063 3388 Dihedral : 7.730 126.378 2740 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.40 % Allowed : 9.22 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2452 helix: -1.40 (0.16), residues: 950 sheet: -2.02 (0.22), residues: 439 loop : -2.36 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.021 0.002 TYR D 390 PHE 0.018 0.001 PHE D 58 TRP 0.005 0.001 TRP A 94 HIS 0.002 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00237 (19388) covalent geometry : angle 0.64163 (26256) hydrogen bonds : bond 0.03704 ( 715) hydrogen bonds : angle 5.01515 ( 2109) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7200 (mmt-90) cc_final: 0.6886 (mmt90) REVERT: A 122 MET cc_start: 0.6847 (mtm) cc_final: 0.6563 (mtt) REVERT: A 418 LYS cc_start: 0.7269 (tptp) cc_final: 0.6999 (tptp) REVERT: A 429 LYS cc_start: 0.8250 (mtmm) cc_final: 0.8038 (mmtt) REVERT: B 120 ARG cc_start: 0.7541 (mtm180) cc_final: 0.7305 (mtm-85) REVERT: B 252 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 41 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 220 GLN cc_start: 0.6950 (tp40) cc_final: 0.6549 (tp-100) REVERT: C 368 MET cc_start: 0.8607 (ttp) cc_final: 0.8404 (ttt) REVERT: C 398 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.6992 (ttm170) REVERT: C 436 LYS cc_start: 0.7269 (tttt) cc_final: 0.6873 (tmtt) REVERT: D 311 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8241 (mtpp) REVERT: D 436 LYS cc_start: 0.7169 (tmtt) cc_final: 0.6742 (tttt) REVERT: E 75 GLU cc_start: 0.6338 (tm-30) cc_final: 0.5916 (tm-30) REVERT: E 113 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7843 (mmp80) REVERT: E 238 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (pt) REVERT: E 311 LYS cc_start: 0.7445 (tptm) cc_final: 0.7229 (ptmm) REVERT: E 411 ASP cc_start: 0.8142 (m-30) cc_final: 0.7901 (m-30) REVERT: E 431 ILE cc_start: 0.8168 (pt) cc_final: 0.7881 (mm) REVERT: F 59 TYR cc_start: 0.8300 (m-80) cc_final: 0.7828 (m-80) REVERT: F 116 ASP cc_start: 0.8023 (t70) cc_final: 0.7590 (t0) outliers start: 49 outliers final: 23 residues processed: 335 average time/residue: 0.1621 time to fit residues: 78.6513 Evaluate side-chains 239 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 132 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 overall best weight: 1.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 416 ASN B 85 HIS B 98 GLN B 152 GLN C 369 HIS D 93 GLN E 98 GLN E 220 GLN E 376 HIS E 416 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115462 restraints weight = 25409.394| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.70 r_work: 0.3070 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19392 Z= 0.153 Angle : 0.665 10.767 26256 Z= 0.320 Chirality : 0.046 0.190 3039 Planarity : 0.005 0.064 3388 Dihedral : 7.491 125.764 2738 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.53 % Allowed : 10.93 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2452 helix: -0.69 (0.17), residues: 948 sheet: -1.82 (0.23), residues: 447 loop : -2.20 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 105 TYR 0.019 0.002 TYR D 390 PHE 0.018 0.001 PHE C 58 TRP 0.005 0.001 TRP E 94 HIS 0.004 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00369 (19388) covalent geometry : angle 0.66506 (26256) hydrogen bonds : bond 0.03850 ( 715) hydrogen bonds : angle 4.69121 ( 2109) Misc. bond : bond 0.00094 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7255 (mmt-90) cc_final: 0.6653 (mmt90) REVERT: A 122 MET cc_start: 0.6953 (mtm) cc_final: 0.6729 (mtt) REVERT: A 201 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 351 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5258 (tt0) REVERT: A 418 LYS cc_start: 0.7250 (tptp) cc_final: 0.6997 (tptp) REVERT: A 429 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7983 (mmtt) REVERT: B 120 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7353 (mtm-85) REVERT: C 41 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8018 (mp) REVERT: C 220 GLN cc_start: 0.7304 (tp40) cc_final: 0.6820 (tp-100) REVERT: C 368 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8603 (ttt) REVERT: C 398 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7089 (ttm170) REVERT: C 436 LYS cc_start: 0.7475 (tttt) cc_final: 0.6950 (tmtt) REVERT: D 311 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8472 (mtpp) REVERT: D 396 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6429 (pp) REVERT: D 399 ILE cc_start: 0.7029 (pp) cc_final: 0.6776 (pt) REVERT: D 436 LYS cc_start: 0.7389 (tmtt) cc_final: 0.6833 (tttt) REVERT: E 75 GLU cc_start: 0.6463 (tm-30) cc_final: 0.5879 (tm-30) REVERT: E 238 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7909 (pt) REVERT: E 311 LYS cc_start: 0.7636 (tptm) cc_final: 0.7164 (ptmm) REVERT: E 431 ILE cc_start: 0.8156 (pt) cc_final: 0.7741 (mm) REVERT: F 52 LYS cc_start: 0.6057 (pttp) cc_final: 0.5457 (tptt) REVERT: F 59 TYR cc_start: 0.8417 (m-80) cc_final: 0.7997 (m-80) REVERT: F 116 ASP cc_start: 0.8201 (t70) cc_final: 0.7912 (t0) REVERT: F 164 LEU cc_start: 0.7685 (mp) cc_final: 0.7381 (mm) outliers start: 72 outliers final: 33 residues processed: 276 average time/residue: 0.1562 time to fit residues: 63.6418 Evaluate side-chains 230 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 129 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS F 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117438 restraints weight = 24965.184| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.72 r_work: 0.3088 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19392 Z= 0.117 Angle : 0.615 9.608 26256 Z= 0.294 Chirality : 0.045 0.356 3039 Planarity : 0.004 0.064 3388 Dihedral : 6.937 121.987 2736 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 12.06 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.16), residues: 2452 helix: -0.13 (0.18), residues: 912 sheet: -1.77 (0.23), residues: 440 loop : -1.93 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.026 0.002 TYR B 390 PHE 0.018 0.001 PHE C 58 TRP 0.003 0.001 TRP E 94 HIS 0.003 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00278 (19388) covalent geometry : angle 0.61529 (26256) hydrogen bonds : bond 0.03335 ( 715) hydrogen bonds : angle 4.48145 ( 2109) Misc. bond : bond 0.00057 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.6597 (mmt90) REVERT: A 122 MET cc_start: 0.6909 (mtm) cc_final: 0.6680 (mtt) REVERT: A 351 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5120 (tt0) REVERT: A 429 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7971 (mmtt) REVERT: B 101 GLU cc_start: 0.7634 (pt0) cc_final: 0.7314 (mt-10) REVERT: B 120 ARG cc_start: 0.7586 (mtm180) cc_final: 0.7337 (mtm-85) REVERT: B 252 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 84 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7592 (mm-30) REVERT: C 220 GLN cc_start: 0.6947 (tp40) cc_final: 0.6531 (tp-100) REVERT: C 368 MET cc_start: 0.8727 (ttp) cc_final: 0.8494 (ttt) REVERT: C 398 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7085 (ttm170) REVERT: C 436 LYS cc_start: 0.7321 (tttt) cc_final: 0.6848 (tmtt) REVERT: D 59 TYR cc_start: 0.8704 (m-80) cc_final: 0.8441 (m-80) REVERT: D 192 ASN cc_start: 0.8160 (t0) cc_final: 0.7925 (t0) REVERT: D 311 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8427 (mtpp) REVERT: D 396 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6540 (pp) REVERT: D 436 LYS cc_start: 0.7258 (tmtt) cc_final: 0.6771 (tttt) REVERT: E 75 GLU cc_start: 0.6246 (tm-30) cc_final: 0.5748 (tm-30) REVERT: E 311 LYS cc_start: 0.7478 (tptm) cc_final: 0.7147 (ptmm) REVERT: E 431 ILE cc_start: 0.8145 (pt) cc_final: 0.7784 (mm) REVERT: F 52 LYS cc_start: 0.6044 (pttp) cc_final: 0.5498 (tptt) REVERT: F 59 TYR cc_start: 0.8301 (m-80) cc_final: 0.7850 (m-80) REVERT: F 116 ASP cc_start: 0.7938 (t70) cc_final: 0.7660 (t0) REVERT: F 120 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6876 (mtm-85) REVERT: F 443 LYS cc_start: 0.6622 (mppt) cc_final: 0.6262 (mmtt) outliers start: 66 outliers final: 36 residues processed: 272 average time/residue: 0.1584 time to fit residues: 63.2604 Evaluate side-chains 235 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 123 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: A 85 HIS B 85 HIS E 416 ASN F 85 HIS F 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108983 restraints weight = 25344.724| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.65 r_work: 0.3030 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 19392 Z= 0.262 Angle : 0.767 11.544 26256 Z= 0.368 Chirality : 0.050 0.317 3039 Planarity : 0.005 0.068 3388 Dihedral : 7.630 120.198 2734 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.17 % Allowed : 12.30 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2452 helix: -0.36 (0.17), residues: 938 sheet: -1.66 (0.23), residues: 448 loop : -1.96 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 113 TYR 0.020 0.002 TYR B 90 PHE 0.021 0.002 PHE A 245 TRP 0.007 0.002 TRP C 94 HIS 0.007 0.002 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00656 (19388) covalent geometry : angle 0.76655 (26256) hydrogen bonds : bond 0.04637 ( 715) hydrogen bonds : angle 4.80608 ( 2109) Misc. bond : bond 0.00201 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 203 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7019 (mmt-90) cc_final: 0.6564 (mmt90) REVERT: B 101 GLU cc_start: 0.7797 (pt0) cc_final: 0.7456 (mt-10) REVERT: B 120 ARG cc_start: 0.7723 (mtm180) cc_final: 0.7419 (mtm-85) REVERT: B 421 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: C 41 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 220 GLN cc_start: 0.6962 (tp40) cc_final: 0.6330 (tp-100) REVERT: C 398 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.6930 (ttm170) REVERT: C 436 LYS cc_start: 0.7376 (tttt) cc_final: 0.6895 (tmtt) REVERT: D 311 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8388 (mtpp) REVERT: D 396 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6829 (pp) REVERT: E 75 GLU cc_start: 0.6367 (tm-30) cc_final: 0.4999 (tt0) REVERT: E 113 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7869 (mmp80) REVERT: E 198 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8079 (mt) REVERT: E 303 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8832 (mp) REVERT: E 311 LYS cc_start: 0.7565 (tptm) cc_final: 0.7319 (ptmt) REVERT: E 420 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (mp) REVERT: E 431 ILE cc_start: 0.8201 (pt) cc_final: 0.7749 (mm) REVERT: F 90 TYR cc_start: 0.8605 (p90) cc_final: 0.8405 (p90) REVERT: F 116 ASP cc_start: 0.8046 (t70) cc_final: 0.7740 (t0) REVERT: F 120 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (mtm-85) REVERT: F 164 LEU cc_start: 0.7777 (mp) cc_final: 0.7535 (mm) REVERT: F 443 LYS cc_start: 0.6630 (mppt) cc_final: 0.6310 (mmtt) outliers start: 85 outliers final: 50 residues processed: 275 average time/residue: 0.1524 time to fit residues: 62.6847 Evaluate side-chains 251 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS C 93 GLN ** F 354 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117936 restraints weight = 25152.357| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.64 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19392 Z= 0.106 Angle : 0.603 8.418 26256 Z= 0.288 Chirality : 0.044 0.219 3039 Planarity : 0.004 0.065 3388 Dihedral : 6.789 106.590 2734 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.38 % Allowed : 13.58 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2452 helix: 0.05 (0.18), residues: 931 sheet: -1.58 (0.24), residues: 431 loop : -1.74 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.020 0.001 TYR B 390 PHE 0.018 0.001 PHE D 58 TRP 0.004 0.001 TRP B 94 HIS 0.003 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00245 (19388) covalent geometry : angle 0.60338 (26256) hydrogen bonds : bond 0.03158 ( 715) hydrogen bonds : angle 4.42658 ( 2109) Misc. bond : bond 0.00044 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 351 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5241 (tt0) REVERT: B 101 GLU cc_start: 0.7636 (pt0) cc_final: 0.7421 (mt-10) REVERT: B 252 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8223 (mt-10) REVERT: B 425 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.6168 (mp10) REVERT: C 41 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7637 (mp) REVERT: C 84 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7653 (mm-30) REVERT: C 220 GLN cc_start: 0.6918 (tp40) cc_final: 0.6447 (tp-100) REVERT: C 368 MET cc_start: 0.8716 (ttp) cc_final: 0.8507 (ttt) REVERT: C 398 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.6980 (ttm170) REVERT: C 436 LYS cc_start: 0.7326 (tttt) cc_final: 0.6887 (tmtt) REVERT: D 59 TYR cc_start: 0.8734 (m-80) cc_final: 0.8417 (m-80) REVERT: D 311 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8302 (mtpp) REVERT: D 396 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6655 (pp) REVERT: D 436 LYS cc_start: 0.7177 (tmtt) cc_final: 0.6690 (tttt) REVERT: E 75 GLU cc_start: 0.6473 (tm-30) cc_final: 0.5805 (tm-30) REVERT: E 311 LYS cc_start: 0.7464 (tptm) cc_final: 0.7213 (ptmm) REVERT: E 420 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8088 (mp) REVERT: E 431 ILE cc_start: 0.8118 (pt) cc_final: 0.7790 (mm) REVERT: F 164 LEU cc_start: 0.7767 (mp) cc_final: 0.7545 (mm) REVERT: F 443 LYS cc_start: 0.6707 (mppt) cc_final: 0.6327 (mmtt) outliers start: 69 outliers final: 43 residues processed: 270 average time/residue: 0.1490 time to fit residues: 59.9855 Evaluate side-chains 243 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 88 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS C 93 GLN ** F 354 HIS ** 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 = 0.3597 r_free = 0.3597 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113547 restraints weight = 25359.693| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.67 r_work: 0.3083 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19392 Z= 0.148 Angle : 0.649 8.943 26256 Z= 0.308 Chirality : 0.046 0.227 3039 Planarity : 0.004 0.066 3388 Dihedral : 6.744 95.982 2734 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 14.07 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2452 helix: 0.07 (0.18), residues: 951 sheet: -1.38 (0.25), residues: 406 loop : -1.78 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.021 0.002 TYR B 390 PHE 0.018 0.001 PHE C 58 TRP 0.010 0.001 TRP D 94 HIS 0.004 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00363 (19388) covalent geometry : angle 0.64891 (26256) hydrogen bonds : bond 0.03580 ( 715) hydrogen bonds : angle 4.47035 ( 2109) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 351 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5297 (tt0) REVERT: A 375 GLU cc_start: 0.6947 (pm20) cc_final: 0.6615 (pm20) REVERT: B 66 ARG cc_start: 0.7928 (ptt180) cc_final: 0.7727 (ptt180) REVERT: B 101 GLU cc_start: 0.7740 (pt0) cc_final: 0.7406 (mt-10) REVERT: C 41 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7894 (mp) REVERT: C 135 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7933 (mmt180) REVERT: C 220 GLN cc_start: 0.6996 (tp40) cc_final: 0.6377 (tp-100) REVERT: C 368 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8596 (ttt) REVERT: C 398 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.6964 (ttm170) REVERT: C 431 ILE cc_start: 0.8617 (pt) cc_final: 0.8329 (pt) REVERT: C 436 LYS cc_start: 0.7396 (tttt) cc_final: 0.6945 (tmtt) REVERT: D 277 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: D 311 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8318 (mtpp) REVERT: D 396 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6674 (pp) REVERT: E 75 GLU cc_start: 0.6504 (tm-30) cc_final: 0.5812 (tm-30) REVERT: E 311 LYS cc_start: 0.7547 (tptm) cc_final: 0.7214 (ptmm) REVERT: E 394 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.4629 (pm20) REVERT: E 420 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8147 (mp) REVERT: E 431 ILE cc_start: 0.8177 (pt) cc_final: 0.7800 (mm) REVERT: F 443 LYS cc_start: 0.6776 (mppt) cc_final: 0.6405 (mmtt) outliers start: 71 outliers final: 46 residues processed: 260 average time/residue: 0.1586 time to fit residues: 60.7644 Evaluate side-chains 245 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 138 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 85 HIS ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** 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 = 0.3590 r_free = 0.3590 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112922 restraints weight = 25329.131| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.73 r_work: 0.3043 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19392 Z= 0.162 Angle : 0.666 9.363 26256 Z= 0.316 Chirality : 0.047 0.369 3039 Planarity : 0.004 0.068 3388 Dihedral : 6.763 91.964 2734 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.38 % Allowed : 14.07 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2452 helix: 0.13 (0.18), residues: 948 sheet: -1.33 (0.27), residues: 369 loop : -1.81 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.021 0.002 TYR B 390 PHE 0.018 0.002 PHE C 58 TRP 0.008 0.001 TRP D 94 HIS 0.005 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00401 (19388) covalent geometry : angle 0.66591 (26256) hydrogen bonds : bond 0.03691 ( 715) hydrogen bonds : angle 4.51074 ( 2109) Misc. bond : bond 0.00088 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7169 (pm20) cc_final: 0.6879 (pm20) REVERT: B 66 ARG cc_start: 0.7882 (ptt180) cc_final: 0.7606 (ptt180) REVERT: B 101 GLU cc_start: 0.7993 (pt0) cc_final: 0.7462 (mt-10) REVERT: B 425 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.6367 (mp10) REVERT: C 41 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 135 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.7854 (mmt180) REVERT: C 220 GLN cc_start: 0.6896 (tp40) cc_final: 0.6249 (tp-100) REVERT: C 398 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.6924 (ttm170) REVERT: C 436 LYS cc_start: 0.7445 (tttt) cc_final: 0.6919 (tmtt) REVERT: D 277 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: D 311 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8371 (mtpp) REVERT: D 396 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6605 (pp) REVERT: D 436 LYS cc_start: 0.7630 (tptp) cc_final: 0.6728 (tttt) REVERT: E 75 GLU cc_start: 0.6490 (tm-30) cc_final: 0.5787 (tm-30) REVERT: E 311 LYS cc_start: 0.7689 (tptm) cc_final: 0.7256 (ptmm) REVERT: E 394 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.4554 (pm20) REVERT: E 420 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8150 (mp) REVERT: E 431 ILE cc_start: 0.8242 (pt) cc_final: 0.7766 (mm) REVERT: F 443 LYS cc_start: 0.6748 (mppt) cc_final: 0.6371 (mmtt) outliers start: 69 outliers final: 54 residues processed: 253 average time/residue: 0.1590 time to fit residues: 59.0298 Evaluate side-chains 252 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 239 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 188 optimal weight: 0.0270 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** F 354 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.148682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123558 restraints weight = 25129.369| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.28 r_work: 0.3140 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19392 Z= 0.119 Angle : 0.620 8.551 26256 Z= 0.294 Chirality : 0.045 0.367 3039 Planarity : 0.004 0.069 3388 Dihedral : 6.324 82.590 2734 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.04 % Allowed : 14.51 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2452 helix: 0.29 (0.18), residues: 952 sheet: -1.25 (0.26), residues: 391 loop : -1.70 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.024 0.001 TYR A 390 PHE 0.017 0.001 PHE C 58 TRP 0.004 0.001 TRP D 94 HIS 0.003 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00285 (19388) covalent geometry : angle 0.62010 (26256) hydrogen bonds : bond 0.03217 ( 715) hydrogen bonds : angle 4.37075 ( 2109) Misc. bond : bond 0.00050 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5315 (tt0) REVERT: A 375 GLU cc_start: 0.6988 (pm20) cc_final: 0.6705 (pm20) REVERT: B 66 ARG cc_start: 0.7727 (ptt180) cc_final: 0.7476 (ptt180) REVERT: B 101 GLU cc_start: 0.7758 (pt0) cc_final: 0.7370 (mt-10) REVERT: B 252 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 362 LEU cc_start: 0.8587 (mm) cc_final: 0.8198 (mt) REVERT: C 41 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 84 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 116 ASP cc_start: 0.7413 (t0) cc_final: 0.7190 (t0) REVERT: C 135 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7887 (mmt180) REVERT: C 220 GLN cc_start: 0.6837 (tp40) cc_final: 0.6331 (tp-100) REVERT: C 328 ASN cc_start: 0.8711 (m110) cc_final: 0.8065 (p0) REVERT: C 368 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8501 (ttt) REVERT: C 398 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.6951 (ttm170) REVERT: C 431 ILE cc_start: 0.8596 (pt) cc_final: 0.8328 (pt) REVERT: C 436 LYS cc_start: 0.7275 (tttt) cc_final: 0.6840 (tmtt) REVERT: D 59 TYR cc_start: 0.8774 (m-80) cc_final: 0.8432 (m-80) REVERT: D 311 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8324 (mtpp) REVERT: D 396 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6731 (pp) REVERT: D 436 LYS cc_start: 0.7434 (tptp) cc_final: 0.6553 (tttt) REVERT: E 75 GLU cc_start: 0.6440 (tm-30) cc_final: 0.5751 (tm-30) REVERT: E 198 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7938 (mt) REVERT: E 311 LYS cc_start: 0.7572 (tptm) cc_final: 0.7179 (ptmm) REVERT: E 394 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.4638 (pm20) REVERT: E 420 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8078 (mp) REVERT: E 431 ILE cc_start: 0.8174 (pt) cc_final: 0.7833 (mm) REVERT: F 443 LYS cc_start: 0.6828 (mppt) cc_final: 0.6484 (mmtt) outliers start: 62 outliers final: 47 residues processed: 253 average time/residue: 0.1624 time to fit residues: 59.8473 Evaluate side-chains 249 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 129 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 119 optimal weight: 0.0040 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117051 restraints weight = 25170.989| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.66 r_work: 0.3113 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19392 Z= 0.107 Angle : 0.603 8.327 26256 Z= 0.286 Chirality : 0.045 0.366 3039 Planarity : 0.004 0.063 3388 Dihedral : 6.030 77.044 2734 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 15.05 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2452 helix: 0.40 (0.18), residues: 970 sheet: -1.14 (0.26), residues: 393 loop : -1.69 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.022 0.001 TYR B 390 PHE 0.016 0.001 PHE D 58 TRP 0.013 0.001 TRP D 94 HIS 0.003 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00253 (19388) covalent geometry : angle 0.60343 (26256) hydrogen bonds : bond 0.03035 ( 715) hydrogen bonds : angle 4.27955 ( 2109) Misc. bond : bond 0.00036 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8212 (ttm) cc_final: 0.7874 (mtm) REVERT: A 351 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5300 (tt0) REVERT: B 101 GLU cc_start: 0.7883 (pt0) cc_final: 0.7435 (mt-10) REVERT: B 252 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 425 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6330 (mp10) REVERT: C 41 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7726 (mp) REVERT: C 84 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7797 (mm-30) REVERT: C 116 ASP cc_start: 0.7579 (t0) cc_final: 0.7304 (t0) REVERT: C 135 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7884 (mmt180) REVERT: C 220 GLN cc_start: 0.6850 (tp40) cc_final: 0.6262 (tp-100) REVERT: C 328 ASN cc_start: 0.8704 (m110) cc_final: 0.8005 (p0) REVERT: C 378 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7465 (ttp-110) REVERT: C 398 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.6992 (ttm170) REVERT: C 431 ILE cc_start: 0.8547 (pt) cc_final: 0.8309 (pt) REVERT: C 436 LYS cc_start: 0.7314 (tttt) cc_final: 0.6841 (tmtt) REVERT: D 59 TYR cc_start: 0.8800 (m-80) cc_final: 0.8452 (m-80) REVERT: D 311 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8314 (mtpp) REVERT: D 436 LYS cc_start: 0.7420 (tptp) cc_final: 0.6451 (tttt) REVERT: E 75 GLU cc_start: 0.6481 (tm-30) cc_final: 0.5831 (tm-30) REVERT: E 198 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7980 (mt) REVERT: E 311 LYS cc_start: 0.7631 (tptm) cc_final: 0.7164 (ptmm) REVERT: E 394 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.4634 (pm20) REVERT: E 420 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8095 (mp) REVERT: E 431 ILE cc_start: 0.8206 (pt) cc_final: 0.7860 (mm) REVERT: F 438 ILE cc_start: 0.7209 (pt) cc_final: 0.6912 (tt) outliers start: 56 outliers final: 45 residues processed: 264 average time/residue: 0.1613 time to fit residues: 62.8372 Evaluate side-chains 252 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 132 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** F 354 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116535 restraints weight = 25298.922| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.78 r_work: 0.3099 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19392 Z= 0.128 Angle : 0.629 8.217 26256 Z= 0.298 Chirality : 0.045 0.399 3039 Planarity : 0.004 0.065 3388 Dihedral : 6.067 76.763 2734 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.70 % Allowed : 15.15 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2452 helix: 0.38 (0.18), residues: 976 sheet: -1.08 (0.26), residues: 393 loop : -1.69 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.022 0.002 TYR B 390 PHE 0.019 0.001 PHE C 133 TRP 0.024 0.002 TRP D 94 HIS 0.004 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00311 (19388) covalent geometry : angle 0.62945 (26256) hydrogen bonds : bond 0.03260 ( 715) hydrogen bonds : angle 4.31137 ( 2109) Misc. bond : bond 0.00051 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3992.65 seconds wall clock time: 69 minutes 37.33 seconds (4177.33 seconds total)