Starting phenix.real_space_refine on Wed Nov 19 21:22:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.map" model { file = "/net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c1o_45126/11_2025/9c1o_45126.cif" } resolution = 3.26 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= 0.007 sd= 0.055 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 18150 2.51 5 N 4740 2.21 5 O 5454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "D" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "E" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "F" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Time building chain proxies: 7.11, per 1000 atoms: 0.25 Number of scatterers: 28416 At special positions: 0 Unit cell: (132.271, 147.117, 144.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 5454 8.00 N 4740 7.00 C 18150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6708 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 17 sheets defined 35.3% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.734A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.623A pdb=" N LYS A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.831A pdb=" N LEU A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 217 " --> pdb=" O TYR A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 217' Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.680A pdb=" N LEU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.861A pdb=" N ARG A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.986A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.568A pdb=" N ILE A 307 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.972A pdb=" N SER A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.515A pdb=" N LEU A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.623A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 454 through 465 removed outlier: 4.111A pdb=" N SER A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.655A pdb=" N VAL A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 501 through 511 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.735A pdb=" N ILE A 522 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 523 " --> pdb=" O SER A 520 " (cutoff:3.500A) Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.520A pdb=" N ARG A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.781A pdb=" N PHE B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.755A pdb=" N LEU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.576A pdb=" N PHE B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.594A pdb=" N GLU B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 240 through 253 removed outlier: 3.731A pdb=" N ASN B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.550A pdb=" N TYR B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.841A pdb=" N ILE B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.577A pdb=" N LEU B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 355 " --> pdb=" O GLU B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.757A pdb=" N LEU B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 421 removed outlier: 3.753A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.090A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.593A pdb=" N THR B 525 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.827A pdb=" N SER B 565 " --> pdb=" O LYS B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.661A pdb=" N GLU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.835A pdb=" N LEU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.874A pdb=" N PHE C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 131 through 135' Processing helix chain 'C' and resid 149 through 162 removed outlier: 3.800A pdb=" N VAL C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.657A pdb=" N GLU C 198 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 199 " --> pdb=" O LYS C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 199' Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.527A pdb=" N LEU C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 233 through 250 removed outlier: 4.045A pdb=" N GLN C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.728A pdb=" N ASN C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 Processing helix chain 'C' and resid 336 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.534A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 removed outlier: 3.576A pdb=" N HIS C 417 " --> pdb=" O PHE C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 418 through 423 Processing helix chain 'C' and resid 457 through 466 Processing helix chain 'C' and resid 485 through 490 removed outlier: 4.426A pdb=" N GLN C 490 " --> pdb=" O THR C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 511 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.636A pdb=" N VAL C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 removed outlier: 3.610A pdb=" N PHE D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.613A pdb=" N LEU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.616A pdb=" N PHE D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 135' Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.862A pdb=" N GLU D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 213 through 217 removed outlier: 4.003A pdb=" N LEU D 216 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET D 217 " --> pdb=" O TYR D 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 213 through 217' Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 233 through 253 removed outlier: 3.603A pdb=" N GLN D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.536A pdb=" N PHE D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 removed outlier: 4.042A pdb=" N ASN D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 306 through 311' Processing helix chain 'D' and resid 321 through 324 Processing helix chain 'D' and resid 335 through 347 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 370 through 380 Processing helix chain 'D' and resid 399 through 424 Processing helix chain 'D' and resid 453 through 465 Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 501 through 512 Processing helix chain 'D' and resid 518 through 523 removed outlier: 4.273A pdb=" N ILE D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.842A pdb=" N SER D 565 " --> pdb=" O HIS D 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 98 through 107 removed outlier: 4.167A pdb=" N LEU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.653A pdb=" N PHE E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 135' Processing helix chain 'E' and resid 148 through 162 removed outlier: 3.551A pdb=" N ALA E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 218 through 227 Processing helix chain 'E' and resid 233 through 251 Processing helix chain 'E' and resid 269 through 282 removed outlier: 3.572A pdb=" N PHE E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 removed outlier: 3.989A pdb=" N ASN E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 321 through 324 Processing helix chain 'E' and resid 335 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.523A pdb=" N LEU E 354 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 380 Processing helix chain 'E' and resid 399 through 424 removed outlier: 3.823A pdb=" N THR E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 removed outlier: 3.692A pdb=" N TYR E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 454 through 465 removed outlier: 3.858A pdb=" N ILE E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 483 Processing helix chain 'E' and resid 484 through 489 Processing helix chain 'E' and resid 501 through 512 Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 559 through 565 Processing helix chain 'E' and resid 572 through 577 removed outlier: 3.578A pdb=" N VAL E 576 " --> pdb=" O SER E 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 98 through 107 removed outlier: 3.984A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 148 through 162 Processing helix chain 'F' and resid 189 through 193 removed outlier: 3.537A pdb=" N PHE F 192 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 193 " --> pdb=" O SER F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 193' Processing helix chain 'F' and resid 195 through 199 removed outlier: 4.121A pdb=" N ASP F 199 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.504A pdb=" N GLN F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 282 Processing helix chain 'F' and resid 304 through 310 removed outlier: 3.894A pdb=" N ILE F 307 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 Processing helix chain 'F' and resid 351 through 355 removed outlier: 3.605A pdb=" N LEU F 354 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 370 through 380 removed outlier: 3.787A pdb=" N ILE F 374 " --> pdb=" O HIS F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 425 removed outlier: 3.802A pdb=" N LYS F 425 " --> pdb=" O LEU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 453 through 465 Processing helix chain 'F' and resid 479 through 483 Processing helix chain 'F' and resid 484 through 489 Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.722A pdb=" N VAL F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 9 removed outlier: 5.600A pdb=" N VAL A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS A 17 " --> pdb=" O VAL A 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 14 through 18 current: chain 'A' and resid 46 through 59 removed outlier: 6.574A pdb=" N PHE A 46 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE A 74 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 48 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 68 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE A 54 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 66 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 56 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 64 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR A 58 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 80 through 82 current: chain 'B' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 14 through 18 current: chain 'B' and resid 45 through 59 removed outlier: 6.938A pdb=" N PHE B 46 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 74 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 48 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 68 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 66 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 56 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 64 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 58 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 80 through 82 current: chain 'C' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 14 through 18 current: chain 'C' and resid 45 through 57 removed outlier: 6.884A pdb=" N PHE C 46 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE C 74 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 48 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 68 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE C 54 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 66 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE C 56 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C 64 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.665A pdb=" N GLY A 117 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 129 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N HIS A 115 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 534 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 180 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU A 438 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE A 182 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN A 203 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 391 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 205 " --> pdb=" O ASP A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.897A pdb=" N PHE B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 542 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 140 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 435 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 203 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASP B 391 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 205 " --> pdb=" O ASP B 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.916A pdb=" N PHE C 127 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 118 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 477 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE C 435 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL C 476 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS C 437 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE C 180 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU C 438 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE C 182 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 179 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE C 390 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 181 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C 203 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ASP C 391 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU C 205 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA8, first strand: chain 'C' and resid 283 through 285 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 9 removed outlier: 6.452A pdb=" N LEU D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 14 through 16 current: chain 'D' and resid 46 through 50 removed outlier: 7.623A pdb=" N PHE D 46 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE D 74 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 48 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 76 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 126 through 130 removed outlier: 7.531A pdb=" N PHE D 127 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 116 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL D 544 " --> pdb=" O CYS D 531 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS D 531 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE D 433 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET D 474 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 435 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL D 476 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS D 437 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 179 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE D 390 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 181 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 203 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 389 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=AB3, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 9 removed outlier: 7.072A pdb=" N LEU E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 14 through 18 current: chain 'E' and resid 47 through 57 removed outlier: 6.815A pdb=" N LEU E 48 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR E 68 " --> pdb=" O GLN E 52 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE E 66 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE E 56 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE E 64 " --> pdb=" O ILE E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 80 current: chain 'F' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 14 through 18 current: chain 'F' and resid 46 through 59 removed outlier: 6.729A pdb=" N PHE F 46 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE F 74 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU F 48 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR F 68 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE F 54 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE F 66 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 56 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE F 64 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 58 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 74 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 76 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 126 through 130 removed outlier: 3.660A pdb=" N GLY E 117 " --> pdb=" O PHE E 127 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 129 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N HIS E 115 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E 180 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU E 438 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE E 182 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE E 179 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE E 390 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 181 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN E 203 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP E 391 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU E 205 " --> pdb=" O ASP E 391 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 283 through 285 Processing sheet with id=AB7, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.857A pdb=" N PHE F 127 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN F 118 " --> pdb=" O LYS F 545 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER F 542 " --> pdb=" O VAL F 533 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 472 " --> pdb=" O PHE F 433 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 435 " --> pdb=" O SER F 472 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU F 438 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 391 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 283 through 285 824 hydrogen bonds defined for protein. 2286 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: 5.60 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9299 1.34 - 1.46: 5341 1.46 - 1.58: 14238 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 28992 Sorted by residual: bond pdb=" CD LYS D 55 " pdb=" CE LYS D 55 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.65e-01 bond pdb=" CA ASN B 218 " pdb=" CB ASN B 218 " ideal model delta sigma weight residual 1.530 1.547 -0.016 1.69e-02 3.50e+03 9.37e-01 bond pdb=" CB ASN B 218 " pdb=" CG ASN B 218 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.35e-01 bond pdb=" CA LYS B 456 " pdb=" C LYS B 456 " ideal model delta sigma weight residual 1.522 1.506 0.016 1.72e-02 3.38e+03 8.34e-01 bond pdb=" CB LYS D 55 " pdb=" CG LYS D 55 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.65e-01 ... (remaining 28987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 38841 2.15 - 4.30: 264 4.30 - 6.45: 19 6.45 - 8.60: 0 8.60 - 10.75: 2 Bond angle restraints: 39126 Sorted by residual: angle pdb=" N ILE D 577 " pdb=" CA ILE D 577 " pdb=" C ILE D 577 " ideal model delta sigma weight residual 113.47 108.46 5.01 1.01e+00 9.80e-01 2.46e+01 angle pdb=" C LEU C 96 " pdb=" CA LEU C 96 " pdb=" CB LEU C 96 " ideal model delta sigma weight residual 115.89 109.79 6.10 1.32e+00 5.74e-01 2.14e+01 angle pdb=" C PRO D 551 " pdb=" N GLU D 552 " pdb=" CA GLU D 552 " ideal model delta sigma weight residual 120.97 131.37 -10.40 2.84e+00 1.24e-01 1.34e+01 angle pdb=" CA LEU F 216 " pdb=" CB LEU F 216 " pdb=" CG LEU F 216 " ideal model delta sigma weight residual 116.30 127.05 -10.75 3.50e+00 8.16e-02 9.43e+00 angle pdb=" C THR F 525 " pdb=" N LEU F 526 " pdb=" CA LEU F 526 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 ... (remaining 39121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 15871 14.95 - 29.90: 1406 29.90 - 44.86: 288 44.86 - 59.81: 74 59.81 - 74.76: 61 Dihedral angle restraints: 17700 sinusoidal: 7392 harmonic: 10308 Sorted by residual: dihedral pdb=" CA TYR C 261 " pdb=" C TYR C 261 " pdb=" N ASP C 262 " pdb=" CA ASP C 262 " ideal model delta harmonic sigma weight residual 180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PHE B 273 " pdb=" C PHE B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LYS C 137 " pdb=" C LYS C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 17697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2805 0.036 - 0.071: 1084 0.071 - 0.107: 309 0.107 - 0.142: 131 0.142 - 0.178: 3 Chirality restraints: 4332 Sorted by residual: chirality pdb=" CA ILE E 64 " pdb=" N ILE E 64 " pdb=" C ILE E 64 " pdb=" CB ILE E 64 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB ILE C 519 " pdb=" CA ILE C 519 " pdb=" CG1 ILE C 519 " pdb=" CG2 ILE C 519 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA VAL C 534 " pdb=" N VAL C 534 " pdb=" C VAL C 534 " pdb=" CB VAL C 534 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 4329 not shown) Planarity restraints: 5082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 293 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO B 294 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 293 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 294 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 294 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 294 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 293 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO E 294 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 294 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 294 " 0.025 5.00e-02 4.00e+02 ... (remaining 5079 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3167 2.75 - 3.29: 26754 3.29 - 3.83: 43510 3.83 - 4.36: 51791 4.36 - 4.90: 90972 Nonbonded interactions: 216194 Sorted by model distance: nonbonded pdb=" O ILE C 411 " pdb=" OH TYR C 469 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS D 55 " pdb=" O THR D 68 " model vdw 2.239 3.120 nonbonded pdb=" O PHE E 106 " pdb=" OG1 THR E 128 " model vdw 2.255 3.040 nonbonded pdb=" O HIS F 561 " pdb=" OG SER F 565 " model vdw 2.265 3.040 nonbonded pdb=" O GLU B 282 " pdb=" ND2 ASN B 332 " model vdw 2.269 3.120 ... (remaining 216189 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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=1.00 max=1.00 mean=1.00 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.002 0.033 28992 Z= 0.096 Angle : 0.469 10.750 39126 Z= 0.255 Chirality : 0.043 0.178 4332 Planarity : 0.004 0.049 5082 Dihedral : 12.739 74.761 10992 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.12 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.08 (0.14), residues: 3498 helix: 0.59 (0.17), residues: 1003 sheet: 0.55 (0.22), residues: 579 loop : -1.94 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 341 TYR 0.021 0.001 TYR D 252 PHE 0.019 0.001 PHE B 273 TRP 0.021 0.001 TRP F 564 HIS 0.004 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00192 (28992) covalent geometry : angle 0.46894 (39126) hydrogen bonds : bond 0.19337 ( 824) hydrogen bonds : angle 6.32561 ( 2286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6220 (mtt) cc_final: 0.6014 (mtt) REVERT: A 116 LEU cc_start: 0.8595 (tp) cc_final: 0.8390 (tt) REVERT: A 139 VAL cc_start: 0.8019 (p) cc_final: 0.7810 (t) REVERT: A 446 ARG cc_start: 0.6910 (ttm170) cc_final: 0.6643 (ttm170) REVERT: A 478 GLN cc_start: 0.7050 (pm20) cc_final: 0.6844 (pm20) REVERT: A 578 MET cc_start: 0.6988 (mtp) cc_final: 0.6779 (mtt) REVERT: B 189 LYS cc_start: 0.7980 (tttt) cc_final: 0.7699 (tttp) REVERT: B 217 MET cc_start: 0.4267 (ttt) cc_final: 0.3235 (mtp) REVERT: B 522 ILE cc_start: 0.7348 (tp) cc_final: 0.7097 (tp) REVERT: B 578 MET cc_start: 0.4060 (mtm) cc_final: 0.3810 (mtm) REVERT: C 6 VAL cc_start: 0.7909 (p) cc_final: 0.7546 (t) REVERT: C 18 ILE cc_start: 0.6779 (mm) cc_final: 0.6534 (tt) REVERT: C 72 VAL cc_start: 0.7981 (m) cc_final: 0.7732 (p) REVERT: C 163 ILE cc_start: 0.7925 (mt) cc_final: 0.7593 (pt) REVERT: C 176 ASN cc_start: 0.6679 (t0) cc_final: 0.6441 (t0) REVERT: C 351 LEU cc_start: 0.7514 (mt) cc_final: 0.7282 (mp) REVERT: C 391 ASP cc_start: 0.7114 (t0) cc_final: 0.6820 (t0) REVERT: D 134 PHE cc_start: 0.7942 (t80) cc_final: 0.7719 (t80) REVERT: E 124 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7699 (mm-30) REVERT: E 184 ILE cc_start: 0.8254 (pt) cc_final: 0.7828 (mt) REVERT: F 376 LYS cc_start: 0.7837 (mttt) cc_final: 0.7598 (mttp) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1975 time to fit residues: 135.8427 Evaluate side-chains 378 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 185 HIS E 170 ASN E 386 ASN F 52 GLN F 103 ASN F 270 ASN F 510 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.211403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167466 restraints weight = 35788.978| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.77 r_work: 0.3697 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28992 Z= 0.244 Angle : 0.650 12.125 39126 Z= 0.345 Chirality : 0.049 0.210 4332 Planarity : 0.005 0.051 5082 Dihedral : 4.661 35.359 3720 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.91 % Rotamer: Outliers : 0.80 % Allowed : 6.30 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.46 (0.14), residues: 3498 helix: 0.13 (0.16), residues: 1057 sheet: 0.38 (0.22), residues: 565 loop : -2.15 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 409 TYR 0.030 0.002 TYR A 261 PHE 0.034 0.002 PHE D 416 TRP 0.043 0.003 TRP F 564 HIS 0.010 0.002 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00615 (28992) covalent geometry : angle 0.64999 (39126) hydrogen bonds : bond 0.07189 ( 824) hydrogen bonds : angle 5.29988 ( 2286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 386 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.6928 (ttm170) cc_final: 0.6654 (ttm170) REVERT: B 95 PHE cc_start: 0.8441 (m-10) cc_final: 0.8090 (m-80) REVERT: B 104 LYS cc_start: 0.7839 (mttt) cc_final: 0.7630 (mttt) REVERT: B 189 LYS cc_start: 0.7957 (tttt) cc_final: 0.7689 (tttp) REVERT: B 217 MET cc_start: 0.4331 (ttt) cc_final: 0.3507 (mtp) REVERT: B 578 MET cc_start: 0.4193 (mtm) cc_final: 0.3972 (mtm) REVERT: C 18 ILE cc_start: 0.6995 (mm) cc_final: 0.6489 (tt) REVERT: C 163 ILE cc_start: 0.8052 (mt) cc_final: 0.7756 (pt) REVERT: C 176 ASN cc_start: 0.6785 (t0) cc_final: 0.6549 (t0) REVERT: C 391 ASP cc_start: 0.7086 (t0) cc_final: 0.6839 (t0) REVERT: D 86 MET cc_start: 0.5723 (mmp) cc_final: 0.5396 (mmp) REVERT: D 416 PHE cc_start: 0.5629 (t80) cc_final: 0.5234 (t80) REVERT: E 124 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7512 (mm-30) REVERT: E 184 ILE cc_start: 0.8259 (pt) cc_final: 0.8012 (mt) REVERT: E 206 ASP cc_start: 0.7034 (p0) cc_final: 0.6790 (p0) REVERT: E 209 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8143 (ptpt) REVERT: F 182 PHE cc_start: 0.7446 (m-10) cc_final: 0.6803 (m-10) REVERT: F 465 GLU cc_start: 0.8401 (pt0) cc_final: 0.7587 (pt0) outliers start: 26 outliers final: 19 residues processed: 398 average time/residue: 0.2011 time to fit residues: 125.6542 Evaluate side-chains 393 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 374 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 562 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 341 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS C 70 GLN ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN E 556 GLN F 103 ASN F 422 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.213933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170564 restraints weight = 35979.220| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.78 r_work: 0.3732 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28992 Z= 0.113 Angle : 0.497 8.545 39126 Z= 0.266 Chirality : 0.044 0.174 4332 Planarity : 0.004 0.046 5082 Dihedral : 4.200 32.857 3720 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.78 % Favored : 92.91 % Rotamer: Outliers : 1.01 % Allowed : 8.49 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.26 (0.14), residues: 3498 helix: 0.41 (0.17), residues: 1065 sheet: 0.50 (0.22), residues: 562 loop : -2.11 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.014 0.001 TYR A 261 PHE 0.018 0.001 PHE E 416 TRP 0.038 0.002 TRP F 564 HIS 0.005 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00255 (28992) covalent geometry : angle 0.49666 (39126) hydrogen bonds : bond 0.04819 ( 824) hydrogen bonds : angle 4.88186 ( 2286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 381 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.7681 (pm20) cc_final: 0.7357 (pm20) REVERT: A 421 LEU cc_start: 0.8306 (tp) cc_final: 0.8050 (tt) REVERT: B 104 LYS cc_start: 0.7822 (mttt) cc_final: 0.7612 (mttt) REVERT: B 189 LYS cc_start: 0.7991 (tttt) cc_final: 0.7715 (tttp) REVERT: B 217 MET cc_start: 0.4296 (ttt) cc_final: 0.3445 (mtp) REVERT: B 554 ARG cc_start: 0.6887 (tmm160) cc_final: 0.6485 (tmm160) REVERT: B 578 MET cc_start: 0.4105 (mtm) cc_final: 0.3891 (mtm) REVERT: C 6 VAL cc_start: 0.7785 (p) cc_final: 0.7560 (t) REVERT: C 18 ILE cc_start: 0.6980 (mm) cc_final: 0.6508 (tt) REVERT: C 55 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7706 (ptpp) REVERT: C 163 ILE cc_start: 0.8018 (mt) cc_final: 0.7710 (pt) REVERT: C 176 ASN cc_start: 0.6746 (t0) cc_final: 0.6497 (t0) REVERT: C 351 LEU cc_start: 0.7493 (mt) cc_final: 0.7138 (mp) REVERT: C 391 ASP cc_start: 0.7084 (t0) cc_final: 0.6850 (t0) REVERT: C 421 LEU cc_start: 0.6798 (pp) cc_final: 0.6466 (mt) REVERT: C 456 LYS cc_start: 0.6080 (tttt) cc_final: 0.5764 (tttt) REVERT: C 573 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6874 (t80) REVERT: D 203 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6258 (m-40) REVERT: D 490 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7270 (mm-40) REVERT: E 124 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7534 (mm-30) REVERT: E 184 ILE cc_start: 0.8275 (pt) cc_final: 0.7831 (mt) REVERT: E 206 ASP cc_start: 0.6973 (p0) cc_final: 0.6713 (p0) REVERT: E 209 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7875 (ptpt) REVERT: E 438 GLU cc_start: 0.6438 (tt0) cc_final: 0.6200 (tt0) REVERT: E 456 LYS cc_start: 0.8426 (tttt) cc_final: 0.8061 (mttm) REVERT: E 559 LYS cc_start: 0.6750 (mmtp) cc_final: 0.6509 (mmtm) outliers start: 33 outliers final: 19 residues processed: 400 average time/residue: 0.2068 time to fit residues: 129.2034 Evaluate side-chains 390 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 369 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 58 optimal weight: 0.0670 chunk 331 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 65 optimal weight: 0.0070 chunk 89 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 234 optimal weight: 0.0970 chunk 315 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 329 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 overall best weight: 0.0692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 185 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN E 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.218542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.175456 restraints weight = 36206.625| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.64 r_work: 0.3820 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28992 Z= 0.083 Angle : 0.441 7.846 39126 Z= 0.234 Chirality : 0.043 0.161 4332 Planarity : 0.003 0.046 5082 Dihedral : 3.744 31.794 3720 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.80 % Favored : 93.88 % Rotamer: Outliers : 1.08 % Allowed : 9.96 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.98 (0.14), residues: 3498 helix: 0.73 (0.17), residues: 1060 sheet: 0.66 (0.23), residues: 546 loop : -1.96 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.013 0.001 TYR F 275 PHE 0.017 0.001 PHE A 416 TRP 0.025 0.001 TRP F 564 HIS 0.006 0.000 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00165 (28992) covalent geometry : angle 0.44094 (39126) hydrogen bonds : bond 0.03050 ( 824) hydrogen bonds : angle 4.47705 ( 2286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 372 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.7609 (pm20) cc_final: 0.7221 (pm20) REVERT: A 537 SER cc_start: 0.8409 (t) cc_final: 0.8085 (p) REVERT: B 104 LYS cc_start: 0.7758 (mttt) cc_final: 0.7545 (mttt) REVERT: B 189 LYS cc_start: 0.8000 (tttt) cc_final: 0.7735 (tttp) REVERT: B 217 MET cc_start: 0.4352 (ttt) cc_final: 0.3492 (mtp) REVERT: B 578 MET cc_start: 0.4070 (mtm) cc_final: 0.3860 (mtm) REVERT: C 6 VAL cc_start: 0.7688 (p) cc_final: 0.7335 (t) REVERT: C 18 ILE cc_start: 0.6884 (mm) cc_final: 0.6585 (tt) REVERT: C 55 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7650 (ptpp) REVERT: C 163 ILE cc_start: 0.7883 (mt) cc_final: 0.7539 (pt) REVERT: C 351 LEU cc_start: 0.7270 (mt) cc_final: 0.7022 (mp) REVERT: C 391 ASP cc_start: 0.7052 (t0) cc_final: 0.6814 (t0) REVERT: C 456 LYS cc_start: 0.6004 (tttt) cc_final: 0.5625 (tttt) REVERT: C 573 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6891 (t80) REVERT: D 490 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7272 (mm-40) REVERT: E 124 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7471 (mm-30) REVERT: E 184 ILE cc_start: 0.8175 (pt) cc_final: 0.7588 (mt) REVERT: E 209 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7858 (ptpt) REVERT: E 398 GLU cc_start: 0.7583 (mp0) cc_final: 0.7350 (mp0) REVERT: E 456 LYS cc_start: 0.8239 (tttt) cc_final: 0.7999 (mttm) outliers start: 35 outliers final: 21 residues processed: 388 average time/residue: 0.2085 time to fit residues: 125.3363 Evaluate side-chains 381 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 359 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 265 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 185 HIS B 235 HIS B 417 HIS B 441 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 HIS D 306 GLN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN F 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165303 restraints weight = 35632.274| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.73 r_work: 0.3670 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 28992 Z= 0.296 Angle : 0.687 13.282 39126 Z= 0.361 Chirality : 0.051 0.229 4332 Planarity : 0.005 0.054 5082 Dihedral : 4.808 30.825 3720 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.23 % Favored : 91.45 % Rotamer: Outliers : 1.78 % Allowed : 10.64 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.14), residues: 3498 helix: 0.27 (0.17), residues: 1032 sheet: 0.33 (0.22), residues: 578 loop : -2.25 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 409 TYR 0.031 0.002 TYR A 261 PHE 0.041 0.003 PHE D 416 TRP 0.057 0.003 TRP F 564 HIS 0.010 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00759 (28992) covalent geometry : angle 0.68659 (39126) hydrogen bonds : bond 0.07405 ( 824) hydrogen bonds : angle 5.09621 ( 2286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 396 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: A 438 GLU cc_start: 0.6997 (tt0) cc_final: 0.6666 (mt-10) REVERT: B 189 LYS cc_start: 0.7977 (tttt) cc_final: 0.7707 (tttp) REVERT: B 554 ARG cc_start: 0.6929 (tmm160) cc_final: 0.6520 (tmm160) REVERT: B 578 MET cc_start: 0.4176 (mtm) cc_final: 0.3959 (mtm) REVERT: C 55 LYS cc_start: 0.8146 (ptpp) cc_final: 0.7811 (ptpp) REVERT: C 163 ILE cc_start: 0.8102 (mt) cc_final: 0.7803 (pt) REVERT: C 351 LEU cc_start: 0.7580 (mt) cc_final: 0.7344 (mp) REVERT: C 391 ASP cc_start: 0.7123 (t0) cc_final: 0.6869 (t0) REVERT: D 86 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5481 (mmt) REVERT: D 490 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7324 (mm-40) REVERT: E 184 ILE cc_start: 0.8234 (pt) cc_final: 0.7925 (mt) REVERT: E 398 GLU cc_start: 0.7948 (mp0) cc_final: 0.7618 (mp0) REVERT: E 456 LYS cc_start: 0.8581 (tttt) cc_final: 0.8271 (mttm) REVERT: F 182 PHE cc_start: 0.7514 (m-10) cc_final: 0.6832 (m-80) REVERT: F 216 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6684 (pt) REVERT: F 465 GLU cc_start: 0.8332 (pt0) cc_final: 0.8101 (pt0) outliers start: 58 outliers final: 38 residues processed: 424 average time/residue: 0.2014 time to fit residues: 133.6332 Evaluate side-chains 429 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 123 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 341 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 325 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS B 441 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN E 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171178 restraints weight = 35743.378| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.77 r_work: 0.3743 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28992 Z= 0.097 Angle : 0.483 7.523 39126 Z= 0.258 Chirality : 0.044 0.175 4332 Planarity : 0.004 0.050 5082 Dihedral : 4.135 31.094 3720 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 1.29 % Allowed : 11.72 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.14), residues: 3498 helix: 0.72 (0.17), residues: 1032 sheet: 0.49 (0.23), residues: 544 loop : -2.13 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.020 0.001 TYR A 507 PHE 0.015 0.001 PHE F 75 TRP 0.043 0.002 TRP F 564 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00209 (28992) covalent geometry : angle 0.48323 (39126) hydrogen bonds : bond 0.04112 ( 824) hydrogen bonds : angle 4.68623 ( 2286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 368 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8530 (tp) cc_final: 0.8304 (tp) REVERT: A 537 SER cc_start: 0.8411 (t) cc_final: 0.8141 (p) REVERT: B 189 LYS cc_start: 0.8042 (tttt) cc_final: 0.7784 (tttp) REVERT: B 554 ARG cc_start: 0.6889 (tmm160) cc_final: 0.6522 (tmm160) REVERT: B 578 MET cc_start: 0.4096 (mtm) cc_final: 0.3868 (mtm) REVERT: C 6 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7605 (t) REVERT: C 18 ILE cc_start: 0.6968 (mm) cc_final: 0.6448 (tt) REVERT: C 163 ILE cc_start: 0.8035 (mt) cc_final: 0.7742 (pt) REVERT: C 280 ASN cc_start: 0.3326 (m110) cc_final: 0.2960 (m110) REVERT: C 351 LEU cc_start: 0.7423 (mt) cc_final: 0.7189 (mp) REVERT: C 391 ASP cc_start: 0.7106 (t0) cc_final: 0.6863 (t0) REVERT: C 573 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6893 (t80) REVERT: D 490 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7270 (mm-40) REVERT: D 575 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6715 (mt-10) REVERT: E 184 ILE cc_start: 0.8193 (pt) cc_final: 0.7748 (mt) REVERT: E 438 GLU cc_start: 0.6460 (tt0) cc_final: 0.6196 (tt0) REVERT: E 456 LYS cc_start: 0.8419 (tttt) cc_final: 0.8207 (mttm) outliers start: 42 outliers final: 26 residues processed: 390 average time/residue: 0.2076 time to fit residues: 126.3429 Evaluate side-chains 395 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 chunk 245 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 377 GLN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN F 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.214627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171149 restraints weight = 35797.746| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.71 r_work: 0.3746 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28992 Z= 0.102 Angle : 0.479 7.925 39126 Z= 0.255 Chirality : 0.044 0.162 4332 Planarity : 0.004 0.050 5082 Dihedral : 3.994 30.699 3720 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.89 % Favored : 92.80 % Rotamer: Outliers : 1.14 % Allowed : 12.52 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.12 (0.14), residues: 3498 helix: 0.69 (0.17), residues: 1061 sheet: 0.58 (0.23), residues: 535 loop : -2.10 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.017 0.001 TYR A 507 PHE 0.016 0.001 PHE C 414 TRP 0.041 0.001 TRP F 564 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00228 (28992) covalent geometry : angle 0.47892 (39126) hydrogen bonds : bond 0.04202 ( 824) hydrogen bonds : angle 4.58860 ( 2286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 375 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 SER cc_start: 0.8295 (t) cc_final: 0.8037 (p) REVERT: B 189 LYS cc_start: 0.8028 (tttt) cc_final: 0.7782 (tttp) REVERT: B 554 ARG cc_start: 0.6877 (tmm160) cc_final: 0.6516 (tmm160) REVERT: B 578 MET cc_start: 0.4097 (mtm) cc_final: 0.3865 (mtm) REVERT: C 6 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7596 (t) REVERT: C 18 ILE cc_start: 0.6971 (mm) cc_final: 0.6472 (tt) REVERT: C 55 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7776 (ptpp) REVERT: C 163 ILE cc_start: 0.8015 (mt) cc_final: 0.7709 (pt) REVERT: C 280 ASN cc_start: 0.3264 (m110) cc_final: 0.2900 (m110) REVERT: C 351 LEU cc_start: 0.7450 (mt) cc_final: 0.7215 (mp) REVERT: C 391 ASP cc_start: 0.7121 (t0) cc_final: 0.6858 (t0) REVERT: C 456 LYS cc_start: 0.6193 (tttt) cc_final: 0.5771 (tttt) REVERT: C 573 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6895 (t80) REVERT: D 490 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7290 (mm-40) REVERT: E 184 ILE cc_start: 0.8180 (pt) cc_final: 0.7737 (mt) REVERT: E 438 GLU cc_start: 0.6447 (tt0) cc_final: 0.6189 (tt0) REVERT: E 456 LYS cc_start: 0.8419 (tttt) cc_final: 0.8134 (mttm) REVERT: F 182 PHE cc_start: 0.7282 (m-10) cc_final: 0.6568 (m-80) REVERT: F 216 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6648 (pt) outliers start: 37 outliers final: 25 residues processed: 397 average time/residue: 0.2045 time to fit residues: 126.5629 Evaluate side-chains 403 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 245 optimal weight: 0.0770 chunk 336 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 201 optimal weight: 50.0000 chunk 194 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 ASN E 170 ASN E 490 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.212511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167735 restraints weight = 35950.953| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.29 r_work: 0.3682 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28992 Z= 0.136 Angle : 0.519 10.078 39126 Z= 0.276 Chirality : 0.045 0.193 4332 Planarity : 0.004 0.052 5082 Dihedral : 4.164 30.413 3720 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.15 % Favored : 92.54 % Rotamer: Outliers : 1.38 % Allowed : 12.70 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.18 (0.14), residues: 3498 helix: 0.67 (0.17), residues: 1052 sheet: 0.59 (0.23), residues: 530 loop : -2.15 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.019 0.001 TYR A 507 PHE 0.024 0.001 PHE B 416 TRP 0.046 0.002 TRP F 564 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00328 (28992) covalent geometry : angle 0.51924 (39126) hydrogen bonds : bond 0.05015 ( 824) hydrogen bonds : angle 4.68971 ( 2286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 SER cc_start: 0.8435 (t) cc_final: 0.8157 (p) REVERT: B 189 LYS cc_start: 0.8038 (tttt) cc_final: 0.7778 (tttp) REVERT: B 554 ARG cc_start: 0.6883 (tmm160) cc_final: 0.6489 (tmm160) REVERT: B 578 MET cc_start: 0.4102 (mtm) cc_final: 0.3856 (mtm) REVERT: C 163 ILE cc_start: 0.8050 (mt) cc_final: 0.7752 (pt) REVERT: C 280 ASN cc_start: 0.3296 (m110) cc_final: 0.2945 (m110) REVERT: C 351 LEU cc_start: 0.7505 (mt) cc_final: 0.7129 (mp) REVERT: C 391 ASP cc_start: 0.7196 (t0) cc_final: 0.6926 (t0) REVERT: C 573 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6855 (t80) REVERT: D 490 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7319 (mm-40) REVERT: D 575 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6837 (mt-10) REVERT: E 184 ILE cc_start: 0.8247 (pt) cc_final: 0.7819 (mt) REVERT: E 438 GLU cc_start: 0.6764 (tt0) cc_final: 0.6542 (tt0) REVERT: E 456 LYS cc_start: 0.8486 (tttt) cc_final: 0.8177 (mttm) REVERT: F 182 PHE cc_start: 0.7378 (m-10) cc_final: 0.6622 (m-80) REVERT: F 216 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6673 (pt) outliers start: 45 outliers final: 33 residues processed: 404 average time/residue: 0.2021 time to fit residues: 127.7388 Evaluate side-chains 413 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 378 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 226 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 321 optimal weight: 30.0000 chunk 291 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.212263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167719 restraints weight = 35753.846| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.34 r_work: 0.3667 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28992 Z= 0.148 Angle : 0.535 10.493 39126 Z= 0.285 Chirality : 0.045 0.205 4332 Planarity : 0.004 0.053 5082 Dihedral : 4.256 29.986 3720 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.40 % Favored : 92.28 % Rotamer: Outliers : 1.41 % Allowed : 12.92 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.23 (0.14), residues: 3498 helix: 0.58 (0.17), residues: 1058 sheet: 0.55 (0.23), residues: 534 loop : -2.16 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.019 0.001 TYR A 507 PHE 0.026 0.001 PHE B 416 TRP 0.048 0.002 TRP F 564 HIS 0.004 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00360 (28992) covalent geometry : angle 0.53530 (39126) hydrogen bonds : bond 0.05211 ( 824) hydrogen bonds : angle 4.71939 ( 2286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 SER cc_start: 0.8467 (t) cc_final: 0.8194 (p) REVERT: B 189 LYS cc_start: 0.8047 (tttt) cc_final: 0.7770 (tttp) REVERT: B 554 ARG cc_start: 0.6880 (tmm160) cc_final: 0.6495 (tmm160) REVERT: B 578 MET cc_start: 0.4072 (mtm) cc_final: 0.3829 (mtm) REVERT: C 6 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7649 (t) REVERT: C 18 ILE cc_start: 0.7249 (mt) cc_final: 0.6480 (tt) REVERT: C 163 ILE cc_start: 0.8066 (mt) cc_final: 0.7769 (pt) REVERT: C 280 ASN cc_start: 0.3299 (m110) cc_final: 0.2954 (m110) REVERT: C 351 LEU cc_start: 0.7525 (mt) cc_final: 0.7151 (mp) REVERT: C 391 ASP cc_start: 0.7209 (t0) cc_final: 0.6946 (t0) REVERT: C 573 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6828 (t80) REVERT: D 490 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7329 (mm-40) REVERT: D 575 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6873 (mt-10) REVERT: E 184 ILE cc_start: 0.8252 (pt) cc_final: 0.7837 (mt) REVERT: E 456 LYS cc_start: 0.8498 (tttt) cc_final: 0.8191 (mttm) REVERT: E 490 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8002 (mp10) REVERT: F 182 PHE cc_start: 0.7406 (m-10) cc_final: 0.6639 (m-80) REVERT: F 216 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6658 (pt) outliers start: 46 outliers final: 35 residues processed: 407 average time/residue: 0.2026 time to fit residues: 128.9259 Evaluate side-chains 417 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 379 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 92 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 chunk 234 optimal weight: 0.1980 chunk 161 optimal weight: 0.1980 chunk 307 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 297 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.215226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172096 restraints weight = 35888.566| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.11 r_work: 0.3739 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28992 Z= 0.088 Angle : 0.463 10.465 39126 Z= 0.245 Chirality : 0.043 0.147 4332 Planarity : 0.004 0.054 5082 Dihedral : 3.824 29.611 3720 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.15 % Favored : 93.60 % Rotamer: Outliers : 0.98 % Allowed : 13.50 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.98 (0.14), residues: 3498 helix: 0.86 (0.17), residues: 1052 sheet: 0.66 (0.23), residues: 537 loop : -2.03 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.014 0.001 TYR A 507 PHE 0.026 0.001 PHE B 416 TRP 0.034 0.001 TRP F 564 HIS 0.003 0.000 HIS D 370 Details of bonding type rmsd covalent geometry : bond 0.00190 (28992) covalent geometry : angle 0.46309 (39126) hydrogen bonds : bond 0.03427 ( 824) hydrogen bonds : angle 4.46024 ( 2286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 SER cc_start: 0.8345 (t) cc_final: 0.8064 (p) REVERT: B 189 LYS cc_start: 0.8057 (tttt) cc_final: 0.7805 (tttp) REVERT: B 578 MET cc_start: 0.4026 (mtm) cc_final: 0.3780 (mtm) REVERT: C 6 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7520 (t) REVERT: C 18 ILE cc_start: 0.7205 (mt) cc_final: 0.6494 (tt) REVERT: C 55 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7794 (ptpp) REVERT: C 163 ILE cc_start: 0.8001 (mt) cc_final: 0.7690 (pt) REVERT: C 351 LEU cc_start: 0.7386 (mt) cc_final: 0.7136 (mp) REVERT: C 391 ASP cc_start: 0.7161 (t0) cc_final: 0.6908 (t0) REVERT: C 456 LYS cc_start: 0.6123 (tttt) cc_final: 0.5662 (tttt) REVERT: C 573 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6862 (t80) REVERT: E 184 ILE cc_start: 0.8210 (pt) cc_final: 0.7694 (mt) REVERT: E 456 LYS cc_start: 0.8407 (tttt) cc_final: 0.8149 (mttm) REVERT: E 490 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7922 (mp10) REVERT: F 182 PHE cc_start: 0.7256 (m-10) cc_final: 0.6624 (m-80) REVERT: F 216 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6618 (pt) outliers start: 32 outliers final: 24 residues processed: 385 average time/residue: 0.2100 time to fit residues: 125.7184 Evaluate side-chains 385 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 358 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 580 TRP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 81 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 chunk 173 optimal weight: 0.0470 chunk 287 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 441 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN E 490 GLN F 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.212307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.169371 restraints weight = 35895.471| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.66 r_work: 0.3725 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28992 Z= 0.150 Angle : 0.536 10.219 39126 Z= 0.284 Chirality : 0.045 0.201 4332 Planarity : 0.004 0.079 5082 Dihedral : 4.189 29.272 3720 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.29 % Favored : 92.45 % Rotamer: Outliers : 1.23 % Allowed : 13.31 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.12 (0.14), residues: 3498 helix: 0.72 (0.17), residues: 1053 sheet: 0.72 (0.24), residues: 517 loop : -2.12 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG F 479 TYR 0.018 0.001 TYR A 507 PHE 0.024 0.001 PHE D 416 TRP 0.050 0.002 TRP F 564 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00367 (28992) covalent geometry : angle 0.53551 (39126) hydrogen bonds : bond 0.05173 ( 824) hydrogen bonds : angle 4.65658 ( 2286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7501.98 seconds wall clock time: 129 minutes 10.62 seconds (7750.62 seconds total)