Starting phenix.real_space_refine on Wed May 28 11:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.map" model { file = "/net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yph_34000/05_2025/7yph_34000.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 19180 2.51 5 N 5345 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.90s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30407 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.33, per 1000 atoms: 0.64 Number of scatterers: 30407 At special positions: 0 Unit cell: (176.79, 157.7, 181.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 6 15.00 O 5769 8.00 N 5345 7.00 C 19180 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: 8.14 Conformation dependent library (CDL) restraints added in 3.8 seconds 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 37 sheets defined 46.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.847A pdb=" N GLN A 148 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 149 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 151' Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.630A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 235 removed outlier: 3.847A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.793A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.930A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.121A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 4.116A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.643A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 removed outlier: 4.075A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 removed outlier: 3.533A pdb=" N GLN A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.361A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.892A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 58 through 62 removed outlier: 4.208A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.181A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.530A pdb=" N LEU B 149 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.548A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 184 through 237 removed outlier: 3.659A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 256 removed outlier: 5.800A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.747A pdb=" N GLU B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 424 through 427 removed outlier: 3.715A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.592A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.654A pdb=" N GLY B 515 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 561 removed outlier: 3.566A pdb=" N GLU B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.503A pdb=" N TYR B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 739 through 744 removed outlier: 4.049A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 768 removed outlier: 4.013A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 119 through 137 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.827A pdb=" N SER C 141 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.948A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 184 through 242 removed outlier: 3.864A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 254 Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.519A pdb=" N ARG C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.260A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.759A pdb=" N ASP C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 removed outlier: 3.892A pdb=" N GLN C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.812A pdb=" N ARG C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 558 Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.731A pdb=" N ILE C 574 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 648 through 651 removed outlier: 3.568A pdb=" N TYR C 651 " --> pdb=" O THR C 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 651' Processing helix chain 'C' and resid 657 through 660 Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 4.321A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.998A pdb=" N GLU C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 764 through 769 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 58 through 62 removed outlier: 3.761A pdb=" N ASP D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 62 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 62' Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.816A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.914A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 153' Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 184 through 238 Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 244 through 256 removed outlier: 4.529A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.280A pdb=" N ARG D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 323 through 336 removed outlier: 3.756A pdb=" N GLU D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.627A pdb=" N GLU D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 434 through 444 removed outlier: 3.573A pdb=" N VAL D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 506 through 515 Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 630 through 647 removed outlier: 4.014A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 removed outlier: 4.019A pdb=" N GLY D 652 " --> pdb=" O GLN D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.675A pdb=" N ASN D 659 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 661 " --> pdb=" O TYR D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 removed outlier: 3.800A pdb=" N ARG D 693 " --> pdb=" O SER D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 728 removed outlier: 4.033A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 removed outlier: 3.914A pdb=" N GLU D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 745 " --> pdb=" O ALA D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 745' Processing helix chain 'D' and resid 750 through 754 Processing helix chain 'D' and resid 761 through 769 removed outlier: 3.967A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 117 through 139 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.857A pdb=" N GLY E 154 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.692A pdb=" N HIS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 185 through 236 removed outlier: 3.511A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 253 removed outlier: 3.638A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.840A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.609A pdb=" N THR E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.710A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.590A pdb=" N LEU E 443 " --> pdb=" O MET E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 494 through 513 removed outlier: 3.735A pdb=" N TYR E 505 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP E 507 " --> pdb=" O ARG E 503 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 523 through 533 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 630 through 647 removed outlier: 4.374A pdb=" N HIS E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 removed outlier: 4.051A pdb=" N VAL E 661 " --> pdb=" O TYR E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 729 removed outlier: 3.719A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 745 removed outlier: 4.260A pdb=" N GLU E 745 " --> pdb=" O ALA E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 removed outlier: 3.960A pdb=" N GLU E 752 " --> pdb=" O LYS E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 769 removed outlier: 3.793A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU E 769 " --> pdb=" O VAL E 765 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 4.317A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 378 through 379 removed outlier: 4.152A pdb=" N ILE A 379 " --> pdb=" O LEU A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.834A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 600 Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 618 Processing sheet with id=AA8, first strand: chain 'A' and resid 733 through 736 removed outlier: 5.849A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.689A pdb=" N LEU B 5 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ARG B 104 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR B 97 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 106 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 95 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN B 93 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.689A pdb=" N LEU B 5 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ARG B 104 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR B 97 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 106 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 95 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN B 93 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 82 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA B 90 " --> pdb=" O GLN B 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 378 through 380 removed outlier: 5.885A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.689A pdb=" N PHE B 451 " --> pdb=" O TYR B 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 623 through 624 removed outlier: 3.593A pdb=" N SER B 624 " --> pdb=" O LEU B 663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AB6, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.542A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 45 Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.552A pdb=" N GLN C 83 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 354 removed outlier: 5.624A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 420 removed outlier: 6.391A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AC3, first strand: chain 'C' and resid 521 through 522 removed outlier: 7.692A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 599 through 600 Processing sheet with id=AC5, first strand: chain 'C' and resid 614 through 615 removed outlier: 3.984A pdb=" N HIS C 664 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 700 through 702 removed outlier: 5.999A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.919A pdb=" N LEU D 5 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 105 " --> pdb=" O LEU D 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 7 through 9 removed outlier: 4.058A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 469 through 470 removed outlier: 6.634A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 379 through 380 removed outlier: 6.272A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 596 through 597 removed outlier: 4.186A pdb=" N GLU D 613 " --> pdb=" O HIS D 666 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 666 " --> pdb=" O GLU D 613 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 615 " --> pdb=" O HIS D 664 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS D 664 " --> pdb=" O ALA D 615 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.371A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'E' and resid 20 through 22 removed outlier: 7.064A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.076A pdb=" N ILE E 350 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 488 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 376 through 377 removed outlier: 6.597A pdb=" N HIS E 377 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 596 through 597 removed outlier: 3.702A pdb=" N ILE E 612 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 701 through 702 removed outlier: 4.030A pdb=" N ALA E 701 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 734 " --> pdb=" O ALA E 701 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 705 through 706 1204 hydrogen bonds defined for protein. 3504 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: 10.71 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 10321 1.35 - 1.50: 7745 1.50 - 1.65: 12673 1.65 - 1.80: 135 1.80 - 1.94: 77 Bond restraints: 30951 Sorted by residual: bond pdb=" C THR B 603 " pdb=" N PRO B 604 " ideal model delta sigma weight residual 1.333 1.385 -0.052 1.44e-02 4.82e+03 1.32e+01 bond pdb=" N THR A 603 " pdb=" CA THR A 603 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.29e+01 bond pdb=" N VAL B 352 " pdb=" CA VAL B 352 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.11e+01 bond pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta sigma weight residual 1.456 1.484 -0.028 8.70e-03 1.32e+04 1.05e+01 bond pdb=" N ILE B 468 " pdb=" CA ILE B 468 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.02e+01 ... (remaining 30946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 40422 3.10 - 6.19: 1286 6.19 - 9.29: 194 9.29 - 12.38: 44 12.38 - 15.48: 8 Bond angle restraints: 41954 Sorted by residual: angle pdb=" C ASP E 324 " pdb=" N VAL E 325 " pdb=" CA VAL E 325 " ideal model delta sigma weight residual 121.97 132.69 -10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ARG B 345 " pdb=" N ASN B 346 " pdb=" CA ASN B 346 " ideal model delta sigma weight residual 121.90 114.49 7.41 1.26e+00 6.30e-01 3.46e+01 angle pdb=" N GLU B 228 " pdb=" CA GLU B 228 " pdb=" CB GLU B 228 " ideal model delta sigma weight residual 110.39 120.04 -9.65 1.66e+00 3.63e-01 3.38e+01 angle pdb=" CA GLU B 423 " pdb=" CB GLU B 423 " pdb=" CG GLU B 423 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" C HIS D 319 " pdb=" N TYR D 320 " pdb=" CA TYR D 320 " ideal model delta sigma weight residual 121.19 129.82 -8.63 1.59e+00 3.96e-01 2.94e+01 ... (remaining 41949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 18548 29.79 - 59.58: 530 59.58 - 89.36: 55 89.36 - 119.15: 1 119.15 - 148.94: 1 Dihedral angle restraints: 19135 sinusoidal: 7985 harmonic: 11150 Sorted by residual: dihedral pdb=" CA ILE C 390 " pdb=" C ILE C 390 " pdb=" N ARG C 391 " pdb=" CA ARG C 391 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA MET D 698 " pdb=" C MET D 698 " pdb=" N ASP D 699 " pdb=" CA ASP D 699 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU B 771 " pdb=" C LEU B 771 " pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 19132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4349 0.117 - 0.234: 397 0.234 - 0.351: 32 0.351 - 0.468: 3 0.468 - 0.585: 1 Chirality restraints: 4782 Sorted by residual: chirality pdb=" CB ILE C 490 " pdb=" CA ILE C 490 " pdb=" CG1 ILE C 490 " pdb=" CG2 ILE C 490 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CB ILE D 308 " pdb=" CA ILE D 308 " pdb=" CG1 ILE D 308 " pdb=" CG2 ILE D 308 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB VAL A 718 " pdb=" CA VAL A 718 " pdb=" CG1 VAL A 718 " pdb=" CG2 VAL A 718 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 4779 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " 0.038 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRP A 298 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 225 " 0.018 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 225 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 225 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 225 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 225 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 225 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 225 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 225 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 203 " 0.029 2.00e-02 2.50e+03 2.64e-02 1.22e+01 pdb=" CG PHE A 203 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 203 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 203 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 203 " 0.000 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2856 2.74 - 3.28: 31215 3.28 - 3.82: 55645 3.82 - 4.36: 65980 4.36 - 4.90: 103885 Nonbonded interactions: 259581 Sorted by model distance: nonbonded pdb=" OG1 THR E 682 " pdb=" O MET E 702 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 648 " pdb=" O PRO B 654 " model vdw 2.208 3.040 nonbonded pdb=" O1A AGS D 801 " pdb=" O2B AGS D 801 " model vdw 2.210 3.040 nonbonded pdb=" O1A AGS B 801 " pdb=" O2G AGS B 801 " model vdw 2.218 3.040 nonbonded pdb=" O THR D 685 " pdb=" OG SER D 689 " model vdw 2.219 3.040 ... (remaining 259576 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 774) selection = chain 'C' selection = (chain 'D' and resid 2 through 774) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 66.710 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.160 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 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 : 0.008 0.106 30951 Z= 0.380 Angle : 1.310 15.480 41954 Z= 0.708 Chirality : 0.071 0.585 4782 Planarity : 0.009 0.081 5457 Dihedral : 14.043 148.938 11955 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.46 % Favored : 91.49 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.12), residues: 3855 helix: -2.00 (0.11), residues: 1578 sheet: -2.52 (0.25), residues: 358 loop : -2.51 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP A 298 HIS 0.023 0.003 HIS B 726 PHE 0.060 0.003 PHE A 203 TYR 0.061 0.003 TYR A 225 ARG 0.028 0.001 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.16507 ( 1203) hydrogen bonds : angle 7.73717 ( 3504) covalent geometry : bond 0.00780 (30951) covalent geometry : angle 1.31010 (41954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 244 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8627 (t0) cc_final: 0.8378 (t0) REVERT: A 226 LEU cc_start: 0.8952 (mt) cc_final: 0.8650 (pp) REVERT: A 401 MET cc_start: 0.8930 (tpp) cc_final: 0.8473 (mmm) REVERT: B 230 MET cc_start: 0.6645 (ppp) cc_final: 0.6287 (ppp) REVERT: B 258 MET cc_start: 0.1242 (mtt) cc_final: 0.0438 (mtt) REVERT: B 496 MET cc_start: 0.9233 (tmm) cc_final: 0.8842 (tmm) REVERT: B 633 MET cc_start: 0.8277 (mpp) cc_final: 0.7972 (mpp) REVERT: B 635 GLU cc_start: 0.8799 (tp30) cc_final: 0.8476 (mm-30) REVERT: C 68 GLN cc_start: 0.8323 (tp40) cc_final: 0.7787 (tp40) REVERT: C 217 MET cc_start: 0.9511 (mmp) cc_final: 0.9310 (mmm) REVERT: C 230 MET cc_start: 0.8532 (ppp) cc_final: 0.8297 (ppp) REVERT: D 258 MET cc_start: 0.4258 (mmm) cc_final: 0.3912 (mmm) REVERT: E 85 MET cc_start: 0.7744 (tpt) cc_final: 0.7329 (tpp) REVERT: E 217 MET cc_start: 0.9016 (mmt) cc_final: 0.8397 (tmm) outliers start: 5 outliers final: 1 residues processed: 248 average time/residue: 0.4329 time to fit residues: 172.0499 Evaluate side-chains 188 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 30.0000 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 638 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN D 138 ASN D 221 GLN D 278 GLN ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.126294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.078017 restraints weight = 101655.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.078022 restraints weight = 100911.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.077791 restraints weight = 95971.024| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30951 Z= 0.212 Angle : 0.796 11.950 41954 Z= 0.406 Chirality : 0.047 0.203 4782 Planarity : 0.006 0.070 5457 Dihedral : 7.821 136.886 4292 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.15 % Favored : 91.83 % Rotamer: Outliers : 0.62 % Allowed : 7.49 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3855 helix: -1.15 (0.12), residues: 1655 sheet: -2.73 (0.24), residues: 371 loop : -2.34 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 292 HIS 0.009 0.002 HIS C 666 PHE 0.020 0.002 PHE C 466 TYR 0.024 0.002 TYR D 643 ARG 0.018 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 1203) hydrogen bonds : angle 6.14635 ( 3504) covalent geometry : bond 0.00448 (30951) covalent geometry : angle 0.79614 (41954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 230 MET cc_start: 0.6495 (ppp) cc_final: 0.6115 (ppp) REVERT: B 258 MET cc_start: 0.2978 (mtt) cc_final: 0.2111 (mtt) REVERT: B 293 LEU cc_start: 0.9217 (tt) cc_final: 0.8825 (mm) REVERT: B 633 MET cc_start: 0.8439 (mpp) cc_final: 0.8072 (mpp) REVERT: C 230 MET cc_start: 0.8446 (ppp) cc_final: 0.8207 (ppp) REVERT: C 401 MET cc_start: 0.7473 (ppp) cc_final: 0.7226 (ppp) REVERT: C 423 GLU cc_start: 0.7688 (tp30) cc_final: 0.7401 (tp30) REVERT: D 258 MET cc_start: 0.4207 (mmm) cc_final: 0.3733 (mmt) REVERT: E 85 MET cc_start: 0.7799 (tpt) cc_final: 0.7527 (tpp) REVERT: E 217 MET cc_start: 0.9311 (mmt) cc_final: 0.8972 (tmm) REVERT: E 427 MET cc_start: 0.3307 (tpt) cc_final: 0.2936 (mmm) outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.4316 time to fit residues: 148.4356 Evaluate side-chains 185 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.0980 chunk 85 optimal weight: 50.0000 chunk 111 optimal weight: 0.0470 chunk 339 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 40.0000 chunk 364 optimal weight: 9.9990 overall best weight: 4.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.122041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.079351 restraints weight = 94782.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.079186 restraints weight = 96664.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.079200 restraints weight = 96434.970| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30951 Z= 0.223 Angle : 0.780 12.777 41954 Z= 0.392 Chirality : 0.047 0.345 4782 Planarity : 0.006 0.075 5457 Dihedral : 7.614 134.208 4290 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.03 % Favored : 90.95 % Rotamer: Outliers : 1.45 % Allowed : 11.40 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.13), residues: 3855 helix: -0.71 (0.12), residues: 1657 sheet: -2.73 (0.24), residues: 370 loop : -2.29 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 292 HIS 0.008 0.001 HIS C 666 PHE 0.020 0.002 PHE C 466 TYR 0.030 0.002 TYR D 643 ARG 0.012 0.001 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 1203) hydrogen bonds : angle 5.83705 ( 3504) covalent geometry : bond 0.00476 (30951) covalent geometry : angle 0.77996 (41954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8488 (mt) cc_final: 0.8194 (pp) REVERT: A 623 LEU cc_start: 0.8513 (tp) cc_final: 0.8120 (pp) REVERT: A 698 MET cc_start: 0.8191 (mmp) cc_final: 0.7957 (mmp) REVERT: B 230 MET cc_start: 0.6420 (ppp) cc_final: 0.6039 (ppp) REVERT: B 372 MET cc_start: 0.6810 (tpt) cc_final: 0.6520 (tpt) REVERT: B 468 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.7078 (tp) REVERT: B 633 MET cc_start: 0.8437 (mpp) cc_final: 0.7952 (mpp) REVERT: B 658 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: C 85 MET cc_start: 0.6983 (tpp) cc_final: 0.6756 (tpp) REVERT: C 423 GLU cc_start: 0.7799 (tp30) cc_final: 0.7524 (tp30) REVERT: C 552 ARG cc_start: 0.7367 (mpt180) cc_final: 0.6835 (tpt170) REVERT: D 258 MET cc_start: 0.4433 (mmm) cc_final: 0.3887 (mmt) REVERT: D 485 MET cc_start: 0.7861 (ppp) cc_final: 0.7171 (ppp) REVERT: E 85 MET cc_start: 0.7805 (tpt) cc_final: 0.7411 (tpp) REVERT: E 427 MET cc_start: 0.2848 (tpt) cc_final: 0.2464 (tpt) outliers start: 47 outliers final: 32 residues processed: 225 average time/residue: 0.4113 time to fit residues: 150.7410 Evaluate side-chains 212 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 179 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 243 optimal weight: 50.0000 chunk 330 optimal weight: 20.0000 chunk 364 optimal weight: 6.9990 chunk 382 optimal weight: 30.0000 chunk 222 optimal weight: 0.9980 chunk 96 optimal weight: 50.0000 chunk 360 optimal weight: 6.9990 chunk 372 optimal weight: 30.0000 chunk 129 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN C 68 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.126489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.077887 restraints weight = 102340.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.077689 restraints weight = 100637.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.077721 restraints weight = 93333.174| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30951 Z= 0.168 Angle : 0.708 11.259 41954 Z= 0.353 Chirality : 0.045 0.217 4782 Planarity : 0.005 0.056 5457 Dihedral : 7.374 132.150 4290 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.96 % Rotamer: Outliers : 1.63 % Allowed : 13.37 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.13), residues: 3855 helix: -0.48 (0.12), residues: 1666 sheet: -2.70 (0.24), residues: 376 loop : -2.19 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.007 0.001 HIS B 407 PHE 0.019 0.001 PHE C 657 TYR 0.022 0.001 TYR D 643 ARG 0.012 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1203) hydrogen bonds : angle 5.55239 ( 3504) covalent geometry : bond 0.00363 (30951) covalent geometry : angle 0.70843 (41954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8083 (mt) cc_final: 0.7669 (pp) REVERT: A 546 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: B 230 MET cc_start: 0.6038 (ppp) cc_final: 0.5734 (ppp) REVERT: B 293 LEU cc_start: 0.9178 (tt) cc_final: 0.8890 (mm) REVERT: B 372 MET cc_start: 0.6648 (tpt) cc_final: 0.6327 (tpt) REVERT: B 439 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8960 (tmm) REVERT: B 633 MET cc_start: 0.8303 (mpp) cc_final: 0.7846 (mpp) REVERT: B 658 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: C 423 GLU cc_start: 0.7834 (tp30) cc_final: 0.7489 (tp30) REVERT: D 258 MET cc_start: 0.4580 (mmm) cc_final: 0.4227 (mmt) REVERT: E 85 MET cc_start: 0.7754 (tpt) cc_final: 0.7481 (tpp) REVERT: E 258 MET cc_start: 0.8079 (ppp) cc_final: 0.7836 (ppp) REVERT: E 683 MET cc_start: -0.4095 (mmt) cc_final: -0.4808 (mtt) outliers start: 53 outliers final: 28 residues processed: 235 average time/residue: 0.4245 time to fit residues: 161.0609 Evaluate side-chains 207 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 19 optimal weight: 50.0000 chunk 155 optimal weight: 6.9990 chunk 376 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.122562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.079199 restraints weight = 93458.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.079177 restraints weight = 94948.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.079173 restraints weight = 95054.188| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30951 Z= 0.199 Angle : 0.735 13.511 41954 Z= 0.365 Chirality : 0.046 0.196 4782 Planarity : 0.005 0.083 5457 Dihedral : 7.364 132.572 4290 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.90 % Favored : 91.08 % Rotamer: Outliers : 2.34 % Allowed : 14.88 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3855 helix: -0.39 (0.12), residues: 1662 sheet: -2.58 (0.25), residues: 373 loop : -2.19 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 563 HIS 0.006 0.001 HIS B 407 PHE 0.017 0.001 PHE C 466 TYR 0.026 0.002 TYR D 643 ARG 0.018 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1203) hydrogen bonds : angle 5.52600 ( 3504) covalent geometry : bond 0.00429 (30951) covalent geometry : angle 0.73488 (41954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8405 (mt) cc_final: 0.8181 (pp) REVERT: A 258 MET cc_start: 0.3823 (tpt) cc_final: 0.3040 (mmm) REVERT: A 546 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: A 623 LEU cc_start: 0.8662 (tp) cc_final: 0.8199 (pp) REVERT: A 698 MET cc_start: 0.8232 (mmp) cc_final: 0.7968 (mmp) REVERT: B 230 MET cc_start: 0.6155 (ppp) cc_final: 0.5766 (ppp) REVERT: B 372 MET cc_start: 0.6855 (tpt) cc_final: 0.6434 (tpt) REVERT: B 633 MET cc_start: 0.8323 (mpp) cc_final: 0.7804 (mpp) REVERT: B 658 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: C 262 VAL cc_start: 0.2334 (OUTLIER) cc_final: 0.1831 (t) REVERT: C 308 ILE cc_start: 0.6927 (tt) cc_final: 0.5935 (tt) REVERT: C 423 GLU cc_start: 0.7780 (tp30) cc_final: 0.7428 (tp30) REVERT: D 258 MET cc_start: 0.4654 (mmm) cc_final: 0.4271 (mmt) REVERT: E 85 MET cc_start: 0.7794 (tpt) cc_final: 0.7399 (tpp) REVERT: E 275 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7868 (ptt-90) REVERT: E 485 MET cc_start: 0.9138 (mpp) cc_final: 0.8572 (pmm) outliers start: 76 outliers final: 50 residues processed: 246 average time/residue: 0.4191 time to fit residues: 167.9419 Evaluate side-chains 230 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 32 optimal weight: 0.7980 chunk 377 optimal weight: 50.0000 chunk 316 optimal weight: 40.0000 chunk 161 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 232 optimal weight: 50.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.080071 restraints weight = 103887.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.077511 restraints weight = 115824.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.077656 restraints weight = 100011.417| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30951 Z= 0.163 Angle : 0.717 21.985 41954 Z= 0.351 Chirality : 0.045 0.260 4782 Planarity : 0.005 0.055 5457 Dihedral : 7.235 131.283 4290 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.16 % Allowed : 16.30 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3855 helix: -0.27 (0.12), residues: 1660 sheet: -2.54 (0.24), residues: 386 loop : -2.13 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.008 0.001 HIS B 407 PHE 0.015 0.001 PHE A 657 TYR 0.021 0.001 TYR D 643 ARG 0.014 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1203) hydrogen bonds : angle 5.35969 ( 3504) covalent geometry : bond 0.00356 (30951) covalent geometry : angle 0.71666 (41954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8844 (mt) cc_final: 0.8599 (pp) REVERT: A 258 MET cc_start: 0.4060 (tpt) cc_final: 0.3332 (mmm) REVERT: A 401 MET cc_start: 0.8822 (tpt) cc_final: 0.8398 (ppp) REVERT: A 546 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 230 MET cc_start: 0.6094 (ppp) cc_final: 0.5249 (ppp) REVERT: B 372 MET cc_start: 0.6799 (tpt) cc_final: 0.6398 (tpt) REVERT: B 626 THR cc_start: 0.7538 (p) cc_final: 0.7281 (p) REVERT: B 633 MET cc_start: 0.8146 (mpp) cc_final: 0.7664 (mpp) REVERT: B 658 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: C 262 VAL cc_start: 0.2617 (OUTLIER) cc_final: 0.2138 (t) REVERT: C 339 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 423 GLU cc_start: 0.7939 (tp30) cc_final: 0.7596 (tp30) REVERT: C 702 MET cc_start: 0.7044 (mpp) cc_final: 0.6592 (mmt) REVERT: D 258 MET cc_start: 0.4506 (mmm) cc_final: 0.4038 (mmt) REVERT: E 85 MET cc_start: 0.7758 (tpt) cc_final: 0.7423 (tpp) REVERT: E 485 MET cc_start: 0.9187 (mpp) cc_final: 0.8551 (mpp) outliers start: 70 outliers final: 49 residues processed: 255 average time/residue: 0.4035 time to fit residues: 168.3588 Evaluate side-chains 231 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 229 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.119547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.078271 restraints weight = 89325.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.078032 restraints weight = 90652.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.077674 restraints weight = 93228.036| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30951 Z= 0.230 Angle : 0.788 19.475 41954 Z= 0.388 Chirality : 0.047 0.282 4782 Planarity : 0.005 0.088 5457 Dihedral : 7.377 132.360 4290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.43 % Allowed : 17.20 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3855 helix: -0.30 (0.13), residues: 1665 sheet: -2.61 (0.24), residues: 379 loop : -2.21 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 563 HIS 0.007 0.002 HIS B 407 PHE 0.021 0.002 PHE C 466 TYR 0.032 0.002 TYR D 643 ARG 0.013 0.001 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 1203) hydrogen bonds : angle 5.51723 ( 3504) covalent geometry : bond 0.00495 (30951) covalent geometry : angle 0.78845 (41954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8589 (mt) cc_final: 0.8387 (pp) REVERT: A 258 MET cc_start: 0.4114 (tpt) cc_final: 0.3361 (mmm) REVERT: A 372 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7677 (ppp) REVERT: A 401 MET cc_start: 0.8751 (tpt) cc_final: 0.8102 (mmm) REVERT: A 546 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: A 623 LEU cc_start: 0.8736 (tp) cc_final: 0.8236 (pp) REVERT: A 666 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8596 (t70) REVERT: B 230 MET cc_start: 0.5739 (ppp) cc_final: 0.5466 (ppp) REVERT: B 633 MET cc_start: 0.8296 (mpp) cc_final: 0.7761 (mpp) REVERT: B 658 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: B 713 MET cc_start: 0.8178 (tpt) cc_final: 0.7968 (tpp) REVERT: C 262 VAL cc_start: 0.2807 (OUTLIER) cc_final: 0.2294 (t) REVERT: C 276 MET cc_start: 0.8760 (tpp) cc_final: 0.8541 (tpp) REVERT: C 385 ARG cc_start: 0.7587 (ppt170) cc_final: 0.7178 (ppt170) REVERT: C 423 GLU cc_start: 0.7932 (tp30) cc_final: 0.7617 (tp30) REVERT: D 258 MET cc_start: 0.4672 (mmm) cc_final: 0.4144 (mmt) REVERT: E 85 MET cc_start: 0.7940 (tpt) cc_final: 0.7498 (tpp) REVERT: E 485 MET cc_start: 0.9156 (mpp) cc_final: 0.8383 (mpp) outliers start: 79 outliers final: 57 residues processed: 250 average time/residue: 0.4065 time to fit residues: 164.7324 Evaluate side-chains 239 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 0.9980 chunk 323 optimal weight: 30.0000 chunk 159 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 337 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 chunk 335 optimal weight: 50.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN E 168 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.144272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.109169 restraints weight = 236570.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.107963 restraints weight = 163691.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.107512 restraints weight = 115689.867| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30951 Z= 0.139 Angle : 0.723 17.788 41954 Z= 0.352 Chirality : 0.045 0.231 4782 Planarity : 0.005 0.055 5457 Dihedral : 7.138 130.794 4290 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.06 % Allowed : 18.15 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3855 helix: -0.21 (0.13), residues: 1681 sheet: -2.55 (0.25), residues: 382 loop : -2.01 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.009 0.001 HIS B 407 PHE 0.014 0.001 PHE A 657 TYR 0.025 0.001 TYR A 768 ARG 0.014 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 1203) hydrogen bonds : angle 5.22355 ( 3504) covalent geometry : bond 0.00305 (30951) covalent geometry : angle 0.72269 (41954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9097 (mt) cc_final: 0.8832 (pp) REVERT: A 258 MET cc_start: 0.3709 (tpt) cc_final: 0.3248 (mmm) REVERT: A 372 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7192 (ppp) REVERT: A 401 MET cc_start: 0.8719 (tpt) cc_final: 0.8287 (ppp) REVERT: A 516 MET cc_start: 0.7173 (ppp) cc_final: 0.5933 (ppp) REVERT: A 541 ARG cc_start: 0.5222 (mmt180) cc_final: 0.4999 (mmt180) REVERT: A 546 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: A 623 LEU cc_start: 0.8759 (tp) cc_final: 0.8358 (pp) REVERT: A 666 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8486 (t70) REVERT: A 745 GLU cc_start: 0.5039 (OUTLIER) cc_final: 0.4779 (tt0) REVERT: B 230 MET cc_start: 0.5745 (ppp) cc_final: 0.5520 (ppp) REVERT: B 293 LEU cc_start: 0.9176 (tt) cc_final: 0.8938 (mm) REVERT: B 633 MET cc_start: 0.8033 (mpp) cc_final: 0.7476 (mpp) REVERT: B 698 MET cc_start: 0.8327 (tpp) cc_final: 0.8087 (tpp) REVERT: C 230 MET cc_start: 0.7714 (ppp) cc_final: 0.7403 (ppp) REVERT: C 262 VAL cc_start: 0.2677 (OUTLIER) cc_final: 0.2183 (t) REVERT: C 423 GLU cc_start: 0.7738 (tp30) cc_final: 0.7422 (tp30) REVERT: C 702 MET cc_start: 0.6999 (mpp) cc_final: 0.6594 (mmt) REVERT: D 258 MET cc_start: 0.4983 (mmm) cc_final: 0.4224 (mmt) REVERT: D 427 MET cc_start: 0.5570 (tmm) cc_final: 0.5288 (tmm) REVERT: E 485 MET cc_start: 0.8897 (mpp) cc_final: 0.8147 (mpp) outliers start: 67 outliers final: 43 residues processed: 246 average time/residue: 0.3989 time to fit residues: 161.0343 Evaluate side-chains 226 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 15 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 chunk 376 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.119467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.077766 restraints weight = 98018.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.077484 restraints weight = 106457.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.077067 restraints weight = 105439.607| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30951 Z= 0.246 Angle : 0.818 16.410 41954 Z= 0.402 Chirality : 0.047 0.232 4782 Planarity : 0.006 0.089 5457 Dihedral : 7.336 131.526 4290 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 29.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.06 % Allowed : 18.64 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3855 helix: -0.25 (0.13), residues: 1678 sheet: -2.53 (0.25), residues: 364 loop : -2.16 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 563 HIS 0.007 0.002 HIS E 18 PHE 0.017 0.002 PHE A 657 TYR 0.033 0.002 TYR D 643 ARG 0.014 0.001 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 1203) hydrogen bonds : angle 5.47087 ( 3504) covalent geometry : bond 0.00531 (30951) covalent geometry : angle 0.81798 (41954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7614 (ppp) REVERT: A 546 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: A 623 LEU cc_start: 0.8628 (tp) cc_final: 0.8116 (pp) REVERT: A 666 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8589 (t70) REVERT: B 230 MET cc_start: 0.5602 (ppp) cc_final: 0.5169 (ppp) REVERT: B 633 MET cc_start: 0.8254 (mpp) cc_final: 0.7971 (mpp) REVERT: C 262 VAL cc_start: 0.2877 (OUTLIER) cc_final: 0.2346 (t) REVERT: C 385 ARG cc_start: 0.7546 (ppt170) cc_final: 0.7197 (ppt170) REVERT: C 423 GLU cc_start: 0.7838 (tp30) cc_final: 0.7470 (tp30) REVERT: C 702 MET cc_start: 0.7060 (mpp) cc_final: 0.6454 (mmt) REVERT: D 258 MET cc_start: 0.4405 (mmm) cc_final: 0.3838 (mmt) REVERT: D 344 VAL cc_start: 0.2475 (OUTLIER) cc_final: 0.2240 (t) REVERT: D 486 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: E 160 MET cc_start: 0.4456 (tpt) cc_final: 0.4045 (tpp) outliers start: 67 outliers final: 53 residues processed: 229 average time/residue: 0.3973 time to fit residues: 150.4785 Evaluate side-chains 233 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 51 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 258 optimal weight: 5.9990 chunk 368 optimal weight: 0.0030 chunk 52 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 309 optimal weight: 30.0000 chunk 141 optimal weight: 3.9990 overall best weight: 3.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.076749 restraints weight = 103415.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.075471 restraints weight = 109372.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.075350 restraints weight = 104649.016| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30951 Z= 0.184 Angle : 0.776 15.882 41954 Z= 0.380 Chirality : 0.046 0.233 4782 Planarity : 0.005 0.078 5457 Dihedral : 7.301 129.414 4290 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.10 % Allowed : 18.86 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3855 helix: -0.23 (0.13), residues: 1676 sheet: -2.61 (0.25), residues: 374 loop : -2.10 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 292 HIS 0.010 0.001 HIS E 168 PHE 0.018 0.001 PHE C 467 TYR 0.024 0.002 TYR A 768 ARG 0.016 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1203) hydrogen bonds : angle 5.37070 ( 3504) covalent geometry : bond 0.00403 (30951) covalent geometry : angle 0.77606 (41954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.4363 (tpt) cc_final: 0.3742 (mmm) REVERT: A 372 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7563 (ppp) REVERT: A 401 MET cc_start: 0.9301 (tpt) cc_final: 0.8468 (ppp) REVERT: A 516 MET cc_start: 0.7302 (ppp) cc_final: 0.6033 (ppp) REVERT: A 541 ARG cc_start: 0.5454 (mmt180) cc_final: 0.5177 (mmt180) REVERT: A 546 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 623 LEU cc_start: 0.8547 (tp) cc_final: 0.8034 (pp) REVERT: A 666 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8584 (t70) REVERT: B 230 MET cc_start: 0.5643 (ppp) cc_final: 0.5262 (ppp) REVERT: B 633 MET cc_start: 0.7991 (mpp) cc_final: 0.7582 (mpp) REVERT: C 262 VAL cc_start: 0.3438 (OUTLIER) cc_final: 0.2967 (t) REVERT: C 423 GLU cc_start: 0.7759 (tp30) cc_final: 0.7451 (tp30) REVERT: C 702 MET cc_start: 0.7191 (mpp) cc_final: 0.6721 (mmt) REVERT: D 258 MET cc_start: 0.4084 (mmm) cc_final: 0.3537 (mmt) REVERT: D 344 VAL cc_start: 0.2019 (OUTLIER) cc_final: 0.1703 (t) REVERT: D 427 MET cc_start: 0.5697 (tmm) cc_final: 0.5483 (tmm) REVERT: D 486 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: D 524 ASP cc_start: 0.9068 (m-30) cc_final: 0.8700 (p0) REVERT: E 327 GLU cc_start: 0.9656 (OUTLIER) cc_final: 0.9341 (mp0) outliers start: 68 outliers final: 56 residues processed: 235 average time/residue: 0.4080 time to fit residues: 157.5748 Evaluate side-chains 238 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 469 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 142 optimal weight: 0.7980 chunk 326 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 373 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 chunk 90 optimal weight: 50.0000 chunk 77 optimal weight: 100.0000 chunk 23 optimal weight: 30.0000 chunk 188 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.080769 restraints weight = 99473.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.080433 restraints weight = 94771.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.080353 restraints weight = 88462.854| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30951 Z= 0.132 Angle : 0.736 15.114 41954 Z= 0.358 Chirality : 0.046 0.237 4782 Planarity : 0.005 0.055 5457 Dihedral : 7.049 129.220 4290 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.79 % Allowed : 19.38 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3855 helix: -0.15 (0.13), residues: 1688 sheet: -2.48 (0.25), residues: 363 loop : -1.97 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 292 HIS 0.008 0.001 HIS B 407 PHE 0.013 0.001 PHE B 466 TYR 0.027 0.001 TYR A 768 ARG 0.010 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1203) hydrogen bonds : angle 5.12507 ( 3504) covalent geometry : bond 0.00293 (30951) covalent geometry : angle 0.73612 (41954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17719.93 seconds wall clock time: 306 minutes 54.83 seconds (18414.83 seconds total)