Starting phenix.real_space_refine on Thu Jun 26 14:53:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yph_34000/06_2025/7yph_34000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yph_34000/06_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_34000/06_2025/7yph_34000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yph_34000/06_2025/7yph_34000.map" model { file = "/net/cci-nas-00/data/ceres_data/7yph_34000/06_2025/7yph_34000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yph_34000/06_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): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.20, per 1000 atoms: 0.60 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: 7.22 Conformation dependent library (CDL) restraints added in 4.1 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: 3.37 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: 10.38 Time building geometry restraints manager: 8.58 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: 3.160 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: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 65.700 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.150 ------------------------------------------------------------------------------- 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 : 3.406 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: 0.4258 time to fit residues: 169.9595 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 : 3.398 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.078155 restraints weight = 101655.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.077862 restraints weight = 98876.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.077937 restraints weight = 93054.347| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 3.107 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: 0.6545 (ppp) cc_final: 0.6151 (ppp) REVERT: B 258 MET cc_start: 0.2820 (mtt) cc_final: 0.1979 (mtt) REVERT: B 293 LEU cc_start: 0.9221 (tt) cc_final: 0.8809 (mm) REVERT: B 633 MET cc_start: 0.8246 (mpp) cc_final: 0.7916 (mpp) REVERT: C 230 MET cc_start: 0.8436 (ppp) cc_final: 0.8199 (ppp) REVERT: C 401 MET cc_start: 0.7423 (ppp) cc_final: 0.7178 (ppp) REVERT: C 423 GLU cc_start: 0.7728 (tp30) cc_final: 0.7430 (tp30) REVERT: D 258 MET cc_start: 0.4243 (mmm) cc_final: 0.3768 (mmt) REVERT: D 336 ARG cc_start: 0.8465 (mmp80) cc_final: 0.8263 (mmm160) REVERT: E 85 MET cc_start: 0.7782 (tpt) cc_final: 0.7508 (tpp) REVERT: E 217 MET cc_start: 0.9306 (mmt) cc_final: 0.8947 (tmm) REVERT: E 427 MET cc_start: 0.3134 (tpt) cc_final: 0.2755 (mmm) outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.4172 time to fit residues: 142.9482 Evaluate side-chains 186 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 3.410 ------------------------------------------------------------------------------- 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: 0.0770 chunk 85 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 364 optimal weight: 9.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.124924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.077227 restraints weight = 105680.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.076733 restraints weight = 109057.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.077038 restraints weight = 103270.584| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30951 Z= 0.211 Angle : 0.763 12.675 41954 Z= 0.385 Chirality : 0.047 0.248 4782 Planarity : 0.006 0.072 5457 Dihedral : 7.579 134.446 4290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.74 % Favored : 91.23 % Rotamer: Outliers : 1.39 % Allowed : 11.19 % Favored : 87.43 % 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: -2.47 (0.13), residues: 3855 helix: -0.70 (0.12), residues: 1656 sheet: -2.71 (0.24), residues: 370 loop : -2.28 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 563 HIS 0.008 0.001 HIS C 666 PHE 0.019 0.002 PHE C 466 TYR 0.028 0.002 TYR D 643 ARG 0.011 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 1203) hydrogen bonds : angle 5.80410 ( 3504) covalent geometry : bond 0.00447 (30951) covalent geometry : angle 0.76293 (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 243 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 3.179 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: 0.8304 (mt) cc_final: 0.8011 (pp) REVERT: A 698 MET cc_start: 0.8293 (mmp) cc_final: 0.8068 (mmp) REVERT: B 230 MET cc_start: 0.6344 (ppp) cc_final: 0.5991 (ppp) REVERT: B 258 MET cc_start: 0.2351 (mtt) cc_final: 0.1782 (mtt) REVERT: B 293 LEU cc_start: 0.9110 (tt) cc_final: 0.8640 (mt) REVERT: B 372 MET cc_start: 0.6723 (tpt) cc_final: 0.6496 (tpt) REVERT: B 468 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7041 (tp) REVERT: B 633 MET cc_start: 0.8289 (mpp) cc_final: 0.7865 (mpp) REVERT: B 658 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: C 423 GLU cc_start: 0.7858 (tp30) cc_final: 0.7578 (tp30) REVERT: C 552 ARG cc_start: 0.7281 (mpt180) cc_final: 0.6726 (tpt170) REVERT: D 258 MET cc_start: 0.4548 (mmm) cc_final: 0.3991 (mmt) REVERT: D 336 ARG cc_start: 0.8466 (mmp80) cc_final: 0.7695 (mmm160) REVERT: D 485 MET cc_start: 0.7972 (ppp) cc_final: 0.7306 (ppp) REVERT: E 85 MET cc_start: 0.7742 (tpt) cc_final: 0.7471 (tpp) REVERT: E 427 MET cc_start: 0.3930 (tpt) cc_final: 0.3548 (tpt) outliers start: 45 outliers final: 30 residues processed: 227 average time/residue: 0.4209 time to fit residues: 154.6474 Evaluate side-chains 212 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 3.576 ------------------------------------------------------------------------------- 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 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 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: 30.0000 chunk 216 optimal weight: 1.9990 chunk 243 optimal weight: 50.0000 chunk 330 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 382 optimal weight: 40.0000 chunk 222 optimal weight: 0.9990 chunk 96 optimal weight: 40.0000 chunk 360 optimal weight: 9.9990 chunk 372 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.117482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.076464 restraints weight = 92954.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.076430 restraints weight = 92026.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.076428 restraints weight = 92204.094| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 30951 Z= 0.285 Angle : 0.842 16.541 41954 Z= 0.423 Chirality : 0.048 0.214 4782 Planarity : 0.006 0.067 5457 Dihedral : 7.735 131.781 4290 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.75 % Favored : 90.22 % Rotamer: Outliers : 2.06 % Allowed : 13.90 % Favored : 84.04 % 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: -2.50 (0.13), residues: 3855 helix: -0.64 (0.12), residues: 1656 sheet: -2.87 (0.24), residues: 375 loop : -2.35 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 563 HIS 0.007 0.002 HIS C 666 PHE 0.021 0.002 PHE C 466 TYR 0.035 0.002 TYR D 643 ARG 0.010 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 1203) hydrogen bonds : angle 5.93656 ( 3504) covalent geometry : bond 0.00608 (30951) covalent geometry : angle 0.84206 (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 251 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.3975 (tpt) cc_final: 0.3046 (mmm) REVERT: A 546 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: A 623 LEU cc_start: 0.8690 (tp) cc_final: 0.8282 (pp) REVERT: B 230 MET cc_start: 0.6158 (ppp) cc_final: 0.5765 (ppp) REVERT: B 439 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8872 (tmm) REVERT: B 633 MET cc_start: 0.8292 (mpp) cc_final: 0.7808 (mpp) REVERT: B 658 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6771 (m-10) REVERT: C 308 ILE cc_start: 0.6945 (tt) cc_final: 0.6483 (tt) REVERT: C 423 GLU cc_start: 0.7940 (tp30) cc_final: 0.7666 (tp30) REVERT: C 552 ARG cc_start: 0.7372 (mpt180) cc_final: 0.6899 (tpt170) REVERT: C 702 MET cc_start: 0.7233 (mtm) cc_final: 0.6970 (mpp) REVERT: D 258 MET cc_start: 0.4999 (mmm) cc_final: 0.4382 (mmt) REVERT: E 85 MET cc_start: 0.7908 (tpt) cc_final: 0.7482 (tpp) REVERT: E 217 MET cc_start: 0.9345 (mmp) cc_final: 0.8939 (tmm) REVERT: E 221 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8978 (pt0) REVERT: E 327 GLU cc_start: 0.9624 (OUTLIER) cc_final: 0.9288 (pm20) REVERT: E 683 MET cc_start: -0.3343 (mmt) cc_final: -0.4213 (mtt) outliers start: 67 outliers final: 44 residues processed: 237 average time/residue: 0.4156 time to fit residues: 160.4767 Evaluate side-chains 215 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 421 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 501 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 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 470 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 384 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 490 ILE 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 D residue 766 LEU Chi-restraints excluded: chain E residue 221 GLN 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: 20.0000 chunk 155 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 323 optimal weight: 50.0000 chunk 113 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 161 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 262 optimal weight: 0.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** 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** D 472 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.125398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.081822 restraints weight = 101000.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.075799 restraints weight = 116846.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.076135 restraints weight = 103303.793| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30951 Z= 0.163 Angle : 0.720 11.161 41954 Z= 0.358 Chirality : 0.046 0.221 4782 Planarity : 0.005 0.063 5457 Dihedral : 7.421 129.512 4290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.07 % Favored : 91.91 % Rotamer: Outliers : 2.28 % Allowed : 15.65 % Favored : 82.06 % 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: -2.23 (0.13), residues: 3855 helix: -0.46 (0.12), residues: 1666 sheet: -2.71 (0.24), residues: 376 loop : -2.17 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.007 0.001 HIS B 407 PHE 0.016 0.001 PHE A 657 TYR 0.019 0.001 TYR D 643 ARG 0.015 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1203) hydrogen bonds : angle 5.51079 ( 3504) covalent geometry : bond 0.00356 (30951) covalent geometry : angle 0.72048 (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 272 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 3.553 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: A 258 MET cc_start: 0.4126 (tpt) cc_final: 0.3350 (mmm) REVERT: A 516 MET cc_start: 0.7246 (ppp) cc_final: 0.5994 (ppp) REVERT: A 546 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: A 698 MET cc_start: 0.8239 (mmp) cc_final: 0.7973 (mmp) REVERT: B 230 MET cc_start: 0.6012 (ppp) cc_final: 0.5584 (ppp) REVERT: B 293 LEU cc_start: 0.9030 (tt) cc_final: 0.8750 (mm) REVERT: B 372 MET cc_start: 0.6774 (tpt) cc_final: 0.6417 (tpt) REVERT: B 633 MET cc_start: 0.8285 (mpp) cc_final: 0.7771 (mpp) REVERT: B 658 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: C 262 VAL cc_start: 0.2872 (OUTLIER) cc_final: 0.2367 (t) REVERT: C 385 ARG cc_start: 0.7428 (ppt170) cc_final: 0.7063 (ppt170) REVERT: C 423 GLU cc_start: 0.7791 (tp30) cc_final: 0.7452 (tp30) REVERT: C 702 MET cc_start: 0.7356 (mtm) cc_final: 0.6676 (mpp) REVERT: D 258 MET cc_start: 0.4292 (mmm) cc_final: 0.3949 (mmt) REVERT: D 344 VAL cc_start: 0.2697 (OUTLIER) cc_final: 0.2381 (t) REVERT: E 85 MET cc_start: 0.7776 (tpt) cc_final: 0.7412 (tpp) outliers start: 74 outliers final: 40 residues processed: 256 average time/residue: 0.4125 time to fit residues: 173.4637 Evaluate side-chains 217 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 3.054 ------------------------------------------------------------------------------- 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 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 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 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 454 HIS Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 93 GLN 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 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 633 MET 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: 10.0000 chunk 377 optimal weight: 50.0000 chunk 316 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 232 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** C 628 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** D 340 GLN D 472 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 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 = 0.4752 r_free = 0.4752 target = 0.122027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.079525 restraints weight = 92597.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.078367 restraints weight = 107395.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.078196 restraints weight = 109135.071| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2572 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= 0.176 Angle : 0.742 22.666 41954 Z= 0.365 Chirality : 0.046 0.237 4782 Planarity : 0.005 0.070 5457 Dihedral : 7.342 131.608 4290 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.53 % Allowed : 17.04 % Favored : 80.43 % 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: -0.34 (0.12), residues: 1669 sheet: -2.57 (0.25), residues: 372 loop : -2.19 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 563 HIS 0.008 0.001 HIS B 407 PHE 0.015 0.001 PHE A 657 TYR 0.024 0.002 TYR D 643 ARG 0.017 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1203) hydrogen bonds : angle 5.43826 ( 3504) covalent geometry : bond 0.00381 (30951) covalent geometry : angle 0.74154 (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 267 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 185 time to evaluate : 3.616 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 258 MET cc_start: 0.4066 (tpt) cc_final: 0.3338 (mmm) REVERT: A 401 MET cc_start: 0.8876 (tpt) cc_final: 0.8497 (ppp) REVERT: A 546 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 623 LEU cc_start: 0.8577 (tp) cc_final: 0.8067 (pp) REVERT: A 666 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (t70) REVERT: B 230 MET cc_start: 0.5893 (ppp) cc_final: 0.5002 (ppp) REVERT: B 293 LEU cc_start: 0.9106 (tt) cc_final: 0.8754 (mt) REVERT: B 372 MET cc_start: 0.6842 (tpt) cc_final: 0.6355 (tpt) REVERT: B 633 MET cc_start: 0.8249 (mpp) cc_final: 0.7691 (mpp) REVERT: B 658 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: C 262 VAL cc_start: 0.2899 (OUTLIER) cc_final: 0.2393 (t) REVERT: C 339 THR cc_start: 0.7352 (OUTLIER) cc_final: 0.7077 (p) REVERT: C 385 ARG cc_start: 0.7527 (ppt170) cc_final: 0.7166 (ppt170) REVERT: C 423 GLU cc_start: 0.7911 (tp30) cc_final: 0.7576 (tp30) REVERT: C 552 ARG cc_start: 0.7342 (mpt180) cc_final: 0.6764 (tpt170) REVERT: D 258 MET cc_start: 0.4474 (mmm) cc_final: 0.3972 (mmt) REVERT: D 328 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8930 (mmt90) REVERT: D 344 VAL cc_start: 0.3349 (OUTLIER) cc_final: 0.2936 (t) REVERT: E 85 MET cc_start: 0.7866 (tpt) cc_final: 0.7419 (tpp) outliers start: 82 outliers final: 59 residues processed: 252 average time/residue: 0.4561 time to fit residues: 188.4099 Evaluate side-chains 240 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 411 GLN 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 694 ARG 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 258 MET 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 381 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 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 293 LEU 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 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 328 ARG 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 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 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 633 MET 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: 9.9990 chunk 1 optimal weight: 50.0000 chunk 229 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 296 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 122 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 151 optimal weight: 0.0060 overall best weight: 2.1402 ------------------------------------------------------------------------------- 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** ** C 628 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 220 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.126484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.078321 restraints weight = 100380.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.077557 restraints weight = 105961.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.077529 restraints weight = 106878.079| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30951 Z= 0.147 Angle : 0.723 20.002 41954 Z= 0.353 Chirality : 0.045 0.221 4782 Planarity : 0.005 0.068 5457 Dihedral : 7.181 130.966 4290 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.40 % Allowed : 17.66 % Favored : 79.94 % 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: -0.27 (0.12), residues: 1679 sheet: -2.49 (0.25), residues: 376 loop : -2.09 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 431 HIS 0.009 0.001 HIS B 407 PHE 0.017 0.001 PHE C 466 TYR 0.032 0.001 TYR E 225 ARG 0.015 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 1203) hydrogen bonds : angle 5.26860 ( 3504) covalent geometry : bond 0.00323 (30951) covalent geometry : angle 0.72257 (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 269 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 191 time to evaluate : 3.567 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: 0.3949 (tpt) cc_final: 0.3325 (mmm) REVERT: A 516 MET cc_start: 0.7292 (ppp) cc_final: 0.6075 (ppp) REVERT: A 546 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 623 LEU cc_start: 0.8655 (tp) cc_final: 0.8174 (pp) REVERT: A 666 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8600 (t70) REVERT: B 230 MET cc_start: 0.5570 (ppp) cc_final: 0.5285 (ppp) REVERT: B 258 MET cc_start: 0.2069 (OUTLIER) cc_final: 0.1317 (mpp) REVERT: B 293 LEU cc_start: 0.9128 (tt) cc_final: 0.8364 (mt) REVERT: B 372 MET cc_start: 0.6638 (tpt) cc_final: 0.6236 (tpt) REVERT: B 479 ARG cc_start: 0.8618 (tpm170) cc_final: 0.8404 (tpm170) REVERT: B 633 MET cc_start: 0.8325 (mpp) cc_final: 0.7815 (mpp) REVERT: B 658 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: C 262 VAL cc_start: 0.3054 (OUTLIER) cc_final: 0.2559 (t) REVERT: C 339 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6765 (p) REVERT: C 423 GLU cc_start: 0.7875 (tp30) cc_final: 0.7489 (tp30) REVERT: D 258 MET cc_start: 0.4047 (mmm) cc_final: 0.3509 (mmt) REVERT: D 344 VAL cc_start: 0.2816 (OUTLIER) cc_final: 0.2442 (t) REVERT: D 427 MET cc_start: 0.5729 (tmm) cc_final: 0.5478 (tmm) REVERT: E 85 MET cc_start: 0.7744 (tpt) cc_final: 0.7432 (tpp) REVERT: E 258 MET cc_start: 0.8090 (ppp) cc_final: 0.7799 (ppp) outliers start: 78 outliers final: 56 residues processed: 254 average time/residue: 0.4192 time to fit residues: 175.4463 Evaluate side-chains 244 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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 409 MET Chi-restraints excluded: chain A residue 411 GLN 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 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 258 MET 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 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 614 VAL Chi-restraints excluded: chain B residue 658 TYR 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 293 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 THR 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 C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 93 GLN 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 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 488 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 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: 3.9990 chunk 323 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 335 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.124531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.077250 restraints weight = 102251.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.076259 restraints weight = 99206.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.076284 restraints weight = 95805.374| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30951 Z= 0.174 Angle : 0.737 17.844 41954 Z= 0.361 Chirality : 0.046 0.273 4782 Planarity : 0.005 0.055 5457 Dihedral : 7.205 133.339 4290 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.62 % Allowed : 17.75 % Favored : 79.63 % 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: -1.96 (0.13), residues: 3855 helix: -0.18 (0.13), residues: 1674 sheet: -2.52 (0.25), residues: 384 loop : -2.10 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.010 0.001 HIS E 168 PHE 0.017 0.001 PHE C 466 TYR 0.026 0.002 TYR D 643 ARG 0.009 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1203) hydrogen bonds : angle 5.29554 ( 3504) covalent geometry : bond 0.00381 (30951) covalent geometry : angle 0.73666 (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 266 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 181 time to evaluate : 3.460 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: 0.4116 (tpt) cc_final: 0.3472 (mmm) REVERT: A 401 MET cc_start: 0.8791 (tpt) cc_final: 0.8191 (mmm) REVERT: A 546 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 623 LEU cc_start: 0.8644 (tp) cc_final: 0.8176 (pp) REVERT: A 666 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8543 (t70) REVERT: B 230 MET cc_start: 0.5556 (ppp) cc_final: 0.5173 (ppp) REVERT: B 372 MET cc_start: 0.6760 (tpt) cc_final: 0.6254 (tpt) REVERT: B 633 MET cc_start: 0.8155 (mpp) cc_final: 0.7688 (mpp) REVERT: B 658 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: C 262 VAL cc_start: 0.3050 (OUTLIER) cc_final: 0.2559 (t) REVERT: C 339 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6987 (p) REVERT: C 423 GLU cc_start: 0.7854 (tp30) cc_final: 0.7503 (tp30) REVERT: C 702 MET cc_start: 0.6964 (mpp) cc_final: 0.6441 (mmt) REVERT: D 258 MET cc_start: 0.4120 (mmm) cc_final: 0.3543 (mmt) REVERT: D 344 VAL cc_start: 0.3070 (OUTLIER) cc_final: 0.2670 (t) REVERT: D 524 ASP cc_start: 0.9091 (m-30) cc_final: 0.8484 (t70) REVERT: E 85 MET cc_start: 0.7760 (tpt) cc_final: 0.7410 (tpp) REVERT: E 258 MET cc_start: 0.8096 (ppp) cc_final: 0.7837 (ppp) REVERT: E 327 GLU cc_start: 0.9648 (OUTLIER) cc_final: 0.9321 (mp0) outliers start: 85 outliers final: 57 residues processed: 250 average time/residue: 0.4224 time to fit residues: 171.7936 Evaluate side-chains 240 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 3.428 ------------------------------------------------------------------------------- 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 411 GLN 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 258 MET 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 412 VAL Chi-restraints excluded: chain B residue 421 LEU 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 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 293 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 359 VAL 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 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 328 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 15 optimal weight: 2.9990 chunk 239 optimal weight: 40.0000 chunk 376 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 341 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 152 optimal weight: 0.0570 chunk 98 optimal weight: 40.0000 overall best weight: 4.6104 ------------------------------------------------------------------------------- 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 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 221 GLN ** 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 = 0.4734 r_free = 0.4734 target = 0.119543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.078316 restraints weight = 89402.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.078089 restraints weight = 89752.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.078089 restraints weight = 91448.340| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30951 Z= 0.210 Angle : 0.783 16.425 41954 Z= 0.385 Chirality : 0.047 0.240 4782 Planarity : 0.005 0.097 5457 Dihedral : 7.331 136.594 4290 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.71 % Allowed : 18.00 % 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: -2.02 (0.13), residues: 3855 helix: -0.23 (0.13), residues: 1676 sheet: -2.49 (0.25), residues: 373 loop : -2.16 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 563 HIS 0.007 0.001 HIS B 407 PHE 0.016 0.002 PHE A 657 TYR 0.030 0.002 TYR D 643 ARG 0.016 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 1203) hydrogen bonds : angle 5.41753 ( 3504) covalent geometry : bond 0.00457 (30951) covalent geometry : angle 0.78296 (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 267 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 179 time to evaluate : 3.772 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 516 MET cc_start: 0.7331 (ppp) cc_final: 0.6111 (ppp) REVERT: A 546 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: A 623 LEU cc_start: 0.8785 (tp) cc_final: 0.8386 (pp) REVERT: A 666 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8612 (t70) REVERT: B 230 MET cc_start: 0.5452 (ppp) cc_final: 0.5200 (ppp) REVERT: B 372 MET cc_start: 0.6800 (tpt) cc_final: 0.6218 (tpt) REVERT: B 439 MET cc_start: 0.8743 (tmm) cc_final: 0.8003 (ppp) REVERT: B 633 MET cc_start: 0.8109 (mpp) cc_final: 0.7592 (mpp) REVERT: B 658 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: C 262 VAL cc_start: 0.3510 (OUTLIER) cc_final: 0.3046 (t) REVERT: C 339 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (p) REVERT: C 385 ARG cc_start: 0.7521 (ppt170) cc_final: 0.7119 (ppt170) REVERT: C 423 GLU cc_start: 0.7830 (tp30) cc_final: 0.7476 (tp30) REVERT: C 552 ARG cc_start: 0.7422 (mpt180) cc_final: 0.6894 (tpt170) REVERT: C 702 MET cc_start: 0.6913 (mpp) cc_final: 0.6298 (mmt) REVERT: D 258 MET cc_start: 0.4510 (mmm) cc_final: 0.3887 (mmt) REVERT: D 427 MET cc_start: 0.5983 (tmm) cc_final: 0.5776 (tmm) REVERT: D 486 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: D 524 ASP cc_start: 0.9322 (m-30) cc_final: 0.8889 (p0) REVERT: E 85 MET cc_start: 0.7977 (tpt) cc_final: 0.7540 (tpp) REVERT: E 160 MET cc_start: 0.4238 (tpt) cc_final: 0.3832 (tpp) outliers start: 88 outliers final: 72 residues processed: 252 average time/residue: 0.4158 time to fit residues: 173.7364 Evaluate side-chains 249 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 3.547 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 411 GLN 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 626 THR 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 703 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 258 MET 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 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET 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 681 ILE 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 293 LEU Chi-restraints excluded: chain C residue 329 ILE 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 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 578 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 138 ASN 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 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: 4.9990 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 368 optimal weight: 0.0770 chunk 52 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 309 optimal weight: 40.0000 chunk 141 optimal weight: 0.7980 overall best weight: 2.7744 ------------------------------------------------------------------------------- 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** ** C 221 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 221 GLN ** 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 = 0.4759 r_free = 0.4759 target = 0.122596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.079506 restraints weight = 92891.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.079198 restraints weight = 95333.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.079088 restraints weight = 96785.220| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30951 Z= 0.163 Angle : 0.753 15.823 41954 Z= 0.367 Chirality : 0.046 0.230 4782 Planarity : 0.005 0.076 5457 Dihedral : 7.248 135.953 4290 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.31 % Allowed : 18.64 % 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: -1.94 (0.14), residues: 3855 helix: -0.21 (0.13), residues: 1682 sheet: -2.59 (0.24), residues: 392 loop : -2.03 (0.15), residues: 1781 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 0.017 0.001 PHE C 466 TYR 0.021 0.001 TYR E 225 ARG 0.017 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1203) hydrogen bonds : angle 5.29070 ( 3504) covalent geometry : bond 0.00360 (30951) covalent geometry : angle 0.75305 (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 258 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 3.389 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 258 MET cc_start: 0.4220 (tpt) cc_final: 0.3711 (mmm) REVERT: A 372 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7435 (ppp) REVERT: A 401 MET cc_start: 0.9322 (tpt) cc_final: 0.8457 (mmm) REVERT: A 516 MET cc_start: 0.7302 (ppp) cc_final: 0.6062 (ppp) REVERT: A 546 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: A 623 LEU cc_start: 0.8644 (tp) cc_final: 0.8237 (pp) REVERT: A 666 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8606 (t70) REVERT: B 230 MET cc_start: 0.5453 (ppp) cc_final: 0.5145 (ppp) REVERT: B 372 MET cc_start: 0.6692 (tpt) cc_final: 0.6223 (tpt) REVERT: B 439 MET cc_start: 0.8411 (tmm) cc_final: 0.7803 (ppp) REVERT: B 633 MET cc_start: 0.8017 (mpp) cc_final: 0.7574 (mpp) REVERT: B 635 GLU cc_start: 0.8832 (tp30) cc_final: 0.8453 (tm-30) REVERT: B 658 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: C 262 VAL cc_start: 0.3349 (OUTLIER) cc_final: 0.2893 (t) REVERT: C 339 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6862 (p) REVERT: C 423 GLU cc_start: 0.7787 (tp30) cc_final: 0.7411 (tp30) REVERT: C 702 MET cc_start: 0.6898 (mpp) cc_final: 0.6542 (mmt) REVERT: D 258 MET cc_start: 0.4143 (mmm) cc_final: 0.3552 (mmt) REVERT: D 427 MET cc_start: 0.5717 (tmm) cc_final: 0.5494 (tmm) REVERT: D 524 ASP cc_start: 0.9304 (m-30) cc_final: 0.8862 (p0) REVERT: E 85 MET cc_start: 0.7901 (tpt) cc_final: 0.7467 (tpp) REVERT: E 160 MET cc_start: 0.4679 (tpt) cc_final: 0.4214 (tpp) REVERT: E 327 GLU cc_start: 0.9653 (OUTLIER) cc_final: 0.9338 (mp0) outliers start: 75 outliers final: 62 residues processed: 243 average time/residue: 0.4131 time to fit residues: 166.2741 Evaluate side-chains 247 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 411 GLN 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 258 MET 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 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 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 229 GLN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU 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 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 578 LEU Chi-restraints excluded: chain C residue 715 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 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 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 142 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 373 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 277 optimal weight: 0.3980 chunk 90 optimal weight: 40.0000 chunk 77 optimal weight: 110.0000 chunk 23 optimal weight: 30.0000 chunk 188 optimal weight: 2.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.120474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.078876 restraints weight = 87737.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.078543 restraints weight = 92284.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.078361 restraints weight = 95309.617| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30951 Z= 0.191 Angle : 0.771 15.170 41954 Z= 0.378 Chirality : 0.046 0.233 4782 Planarity : 0.005 0.079 5457 Dihedral : 7.312 137.826 4290 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.53 % Allowed : 18.55 % Favored : 78.92 % 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: -1.99 (0.13), residues: 3855 helix: -0.20 (0.13), residues: 1681 sheet: -2.62 (0.24), residues: 392 loop : -2.10 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 563 HIS 0.007 0.001 HIS B 407 PHE 0.018 0.002 PHE A 203 TYR 0.026 0.002 TYR D 643 ARG 0.016 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1203) hydrogen bonds : angle 5.35816 ( 3504) covalent geometry : bond 0.00421 (30951) covalent geometry : angle 0.77080 (41954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17526.63 seconds wall clock time: 301 minutes 56.39 seconds (18116.39 seconds total)