Starting phenix.real_space_refine on Fri Mar 6 11:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuw_34113/03_2026/7yuw_34113.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 8 5.49 5 S 105 5.16 5 C 19230 2.51 5 N 5355 2.21 5 O 5785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30483 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.24 Number of scatterers: 30483 At special positions: 0 Unit cell: (195.98, 157.44, 168.92, 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 105 16.00 P 8 15.00 O 5785 8.00 N 5355 7.00 C 19230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.1 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: 143 helices and 39 sheets defined 46.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 4.294A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.609A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 235 removed outlier: 3.736A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.581A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.505A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.236A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.904A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.174A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.554A pdb=" N LEU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.019A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.653A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.675A pdb=" N ARG A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 4.114A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.651A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.641A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.985A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.718A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.509A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.806A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.812A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.680A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.866A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 237 removed outlier: 4.134A pdb=" N TYR B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.935A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.583A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.920A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 440 removed outlier: 4.356A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.842A pdb=" N ALA B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.755A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 631 through 646 Processing helix chain 'B' and resid 647 through 651 removed outlier: 3.710A pdb=" N TYR B 651 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.501A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.550A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.813A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.889A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.704A pdb=" N GLU C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.731A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.705A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 236 removed outlier: 3.670A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 removed outlier: 3.543A pdb=" N ARG C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.816A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 360 through 371 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.607A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.398A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.960A pdb=" N ASP C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 503 Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.755A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.673A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.874A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 727 Processing helix chain 'C' and resid 736 through 738 No H-bonds generated for 'chain 'C' and resid 736 through 738' Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.638A pdb=" N GLU C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.720A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 4.274A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.669A pdb=" N LYS D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.543A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.570A pdb=" N ILE D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 238 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.519A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.514A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 removed outlier: 4.140A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 4.201A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.506A pdb=" N ASP D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.199A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.984A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.978A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.536A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.849A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 removed outlier: 3.547A pdb=" N GLU D 589 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR D 590 " --> pdb=" O LYS D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 586 through 590' Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.500A pdb=" N HIS D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.550A pdb=" N LYS D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 724 removed outlier: 3.525A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 744 removed outlier: 5.054A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 770 removed outlier: 4.120A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 117 through 139 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.804A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 233 removed outlier: 4.040A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.543A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.581A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 360 through 373 removed outlier: 3.527A pdb=" N LEU E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.616A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.558A pdb=" N ASN E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 494 through 514 removed outlier: 5.176A 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 535 removed outlier: 3.568A pdb=" N ILE E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.700A pdb=" N GLU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 removed outlier: 4.336A pdb=" N LYS E 587 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 647 removed outlier: 3.894A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 651 Processing helix chain 'E' and resid 656 through 659 removed outlier: 3.528A pdb=" N ASN E 659 " --> pdb=" O ASP E 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 659' Processing helix chain 'E' and resid 679 through 691 Processing helix chain 'E' and resid 717 through 728 Processing helix chain 'E' and resid 738 through 743 removed outlier: 4.577A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 7.357A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (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 377 through 380 removed outlier: 6.222A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.294A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.617A pdb=" N VAL A 665 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.907A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 735 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 759 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.791A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 25 removed outlier: 7.056A pdb=" N LEU B 82 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.468A pdb=" N ARG B 104 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 470 through 471 removed outlier: 5.595A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 378 removed outlier: 6.756A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 597 through 603 removed outlier: 3.731A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 599 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 614 through 615 removed outlier: 6.889A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.540A pdb=" N VAL B 734 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.583A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 20 through 22 removed outlier: 5.382A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 354 removed outlier: 6.434A 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 376 through 378 removed outlier: 6.608A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.575A pdb=" N ILE C 569 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 592 through 593 removed outlier: 3.805A pdb=" N GLN C 593 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 597 through 601 removed outlier: 4.161A pdb=" N ALA C 597 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 665 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 705 through 707 removed outlier: 3.550A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.464A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.696A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN D 83 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 74 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AC9, first strand: chain 'D' and resid 377 through 378 removed outlier: 3.725A pdb=" N HIS D 377 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 420 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AD2, first strand: chain 'D' and resid 596 through 598 removed outlier: 3.525A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 612 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 622 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 601 through 603 removed outlier: 3.667A pdb=" N THR D 608 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.219A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 705 through 707 Processing sheet with id=AD6, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.246A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 104 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.246A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 104 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.671A pdb=" N ASP E 422 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.780A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 597 through 603 removed outlier: 4.224A pdb=" N ALA E 601 " --> pdb=" O THR E 608 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR E 608 " --> pdb=" O ALA E 601 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 603 " --> pdb=" O GLY E 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 701 through 702 removed outlier: 6.398A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 705 through 707 removed outlier: 3.635A pdb=" N GLU E 705 " --> pdb=" O MET E 713 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 711 " --> pdb=" O SER E 707 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3672 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: 6.03 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8610 1.33 - 1.45: 4540 1.45 - 1.57: 17664 1.57 - 1.70: 12 1.70 - 1.82: 210 Bond restraints: 31036 Sorted by residual: bond pdb=" N LEU E 246 " pdb=" CA LEU E 246 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N ILE E 233 " pdb=" CA ILE E 233 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.33e+00 bond pdb=" N ASP D 241 " pdb=" CA ASP D 241 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.27e+00 bond pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.88e+00 bond pdb=" N LEU C 243 " pdb=" CA LEU C 243 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.71e+00 ... (remaining 31031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 40620 1.88 - 3.76: 1244 3.76 - 5.63: 171 5.63 - 7.51: 35 7.51 - 9.39: 10 Bond angle restraints: 42080 Sorted by residual: angle pdb=" N VAL D 762 " pdb=" CA VAL D 762 " pdb=" C VAL D 762 " ideal model delta sigma weight residual 111.91 105.57 6.34 8.90e-01 1.26e+00 5.08e+01 angle pdb=" N ILE B 308 " pdb=" CA ILE B 308 " pdb=" C ILE B 308 " ideal model delta sigma weight residual 113.47 106.60 6.87 1.01e+00 9.80e-01 4.63e+01 angle pdb=" N LEU A 246 " pdb=" CA LEU A 246 " pdb=" C LEU A 246 " ideal model delta sigma weight residual 111.82 104.76 7.06 1.16e+00 7.43e-01 3.70e+01 angle pdb=" C ARG C 250 " pdb=" N LYS C 251 " pdb=" CA LYS C 251 " ideal model delta sigma weight residual 120.29 112.48 7.81 1.42e+00 4.96e-01 3.03e+01 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 111.48 107.05 4.43 9.40e-01 1.13e+00 2.22e+01 ... (remaining 42075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 18826 33.01 - 66.02: 269 66.02 - 99.04: 51 99.04 - 132.05: 2 132.05 - 165.06: 1 Dihedral angle restraints: 19149 sinusoidal: 7994 harmonic: 11155 Sorted by residual: dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -133.15 -46.85 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual 180.00 -134.99 -45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA ASP A 51 " pdb=" C ASP A 51 " pdb=" N PRO A 52 " pdb=" CA PRO A 52 " ideal model delta harmonic sigma weight residual 180.00 -144.45 -35.55 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 19146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4126 0.067 - 0.134: 625 0.134 - 0.201: 32 0.201 - 0.267: 2 0.267 - 0.334: 1 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CB ILE B 379 " pdb=" CA ILE B 379 " pdb=" CG1 ILE B 379 " pdb=" CG2 ILE B 379 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA LEU A 246 " pdb=" N LEU A 246 " pdb=" C LEU A 246 " pdb=" CB LEU A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE E 233 " pdb=" CA ILE E 233 " pdb=" CG1 ILE E 233 " pdb=" CG2 ILE E 233 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4783 not shown) Planarity restraints: 5464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 603 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO D 604 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 604 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 604 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 51 " 0.058 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 52 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 444 " 0.053 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO D 445 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 445 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 445 " 0.044 5.00e-02 4.00e+02 ... (remaining 5461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 779 2.69 - 3.25: 30615 3.25 - 3.80: 47749 3.80 - 4.35: 63197 4.35 - 4.90: 102430 Nonbonded interactions: 244770 Sorted by model distance: nonbonded pdb=" O TYR C 493 " pdb=" OG1 THR C 494 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR E 626 " pdb=" O VAL E 665 " model vdw 2.175 3.040 nonbonded pdb=" O PRO B 402 " pdb=" NH2 ARG C 432 " model vdw 2.182 3.120 nonbonded pdb=" O GLN E 277 " pdb=" OG1 THR E 284 " model vdw 2.186 3.040 nonbonded pdb=" O TYR B 493 " pdb=" OG1 THR B 494 " model vdw 2.188 3.040 ... (remaining 244765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.200 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.004 0.055 31036 Z= 0.209 Angle : 0.764 9.388 42080 Z= 0.438 Chirality : 0.046 0.334 4786 Planarity : 0.006 0.093 5464 Dihedral : 12.959 165.062 11969 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 0.15 % Allowed : 0.40 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3855 helix: -0.04 (0.13), residues: 1649 sheet: -2.60 (0.23), residues: 455 loop : -2.33 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 529 TYR 0.022 0.001 TYR A 493 PHE 0.011 0.001 PHE E 557 TRP 0.033 0.002 TRP B 292 HIS 0.005 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00381 (31036) covalent geometry : angle 0.76370 (42080) hydrogen bonds : bond 0.16841 ( 1266) hydrogen bonds : angle 6.84997 ( 3672) *********************** 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 353 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 348 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3422 (p90) cc_final: 0.2829 (p90) REVERT: B 85 MET cc_start: 0.4867 (mmt) cc_final: 0.4460 (mmt) REVERT: B 488 ILE cc_start: 0.7868 (mm) cc_final: 0.7377 (mt) REVERT: C 378 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.7868 (ttt180) REVERT: D 419 ILE cc_start: 0.8583 (mm) cc_final: 0.8374 (mm) REVERT: E 85 MET cc_start: 0.5286 (mpp) cc_final: 0.4081 (mpp) REVERT: E 258 MET cc_start: 0.4479 (tpp) cc_final: 0.4174 (tpp) outliers start: 5 outliers final: 1 residues processed: 353 average time/residue: 0.1794 time to fit residues: 106.3737 Evaluate side-chains 271 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 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 ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 220 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 447 GLN E 495 ASN E 666 HIS E 727 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.209984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.149098 restraints weight = 61984.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148581 restraints weight = 39558.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.149878 restraints weight = 26843.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150862 restraints weight = 21657.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.151187 restraints weight = 19241.226| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31036 Z= 0.259 Angle : 0.780 10.282 42080 Z= 0.390 Chirality : 0.048 0.275 4786 Planarity : 0.006 0.067 5464 Dihedral : 7.813 172.901 4301 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.60 % Favored : 90.30 % Rotamer: Outliers : 1.29 % Allowed : 7.92 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 3855 helix: -0.25 (0.13), residues: 1699 sheet: -2.52 (0.23), residues: 434 loop : -2.51 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 91 TYR 0.038 0.002 TYR C 768 PHE 0.023 0.002 PHE C 657 TRP 0.016 0.002 TRP E 65 HIS 0.008 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00596 (31036) covalent geometry : angle 0.77978 (42080) hydrogen bonds : bond 0.04813 ( 1266) hydrogen bonds : angle 5.75703 ( 3672) *********************** 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 330 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 488 ILE cc_start: 0.8003 (mm) cc_final: 0.7509 (mt) REVERT: B 496 MET cc_start: 0.8076 (tpp) cc_final: 0.7822 (tpp) REVERT: B 694 ARG cc_start: 0.7178 (mmt180) cc_final: 0.6892 (mmm160) REVERT: C 160 MET cc_start: 0.4369 (tmm) cc_final: 0.4167 (mpp) REVERT: C 230 MET cc_start: 0.8568 (tmm) cc_final: 0.8301 (tmm) REVERT: C 625 LEU cc_start: 0.8409 (mt) cc_final: 0.8143 (mt) REVERT: E 85 MET cc_start: 0.4832 (mpp) cc_final: 0.3828 (mpp) REVERT: E 372 MET cc_start: 0.8130 (mmm) cc_final: 0.7845 (mmm) REVERT: E 496 MET cc_start: 0.7235 (mmm) cc_final: 0.6969 (mmm) REVERT: E 631 GLU cc_start: 0.7508 (tp30) cc_final: 0.6710 (tp30) REVERT: E 635 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8068 (mm-30) outliers start: 42 outliers final: 27 residues processed: 312 average time/residue: 0.1804 time to fit residues: 95.0630 Evaluate side-chains 282 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 304 optimal weight: 1.9990 chunk 359 optimal weight: 20.0000 chunk 174 optimal weight: 40.0000 chunk 290 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 322 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 224 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 739 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.212012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151106 restraints weight = 62541.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150657 restraints weight = 39578.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152176 restraints weight = 29085.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.154151 restraints weight = 19957.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.153954 restraints weight = 18407.440| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31036 Z= 0.172 Angle : 0.679 8.738 42080 Z= 0.338 Chirality : 0.045 0.284 4786 Planarity : 0.005 0.062 5464 Dihedral : 7.455 160.968 4299 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.96 % Favored : 91.96 % Rotamer: Outliers : 1.69 % Allowed : 10.32 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3855 helix: -0.05 (0.13), residues: 1688 sheet: -2.47 (0.23), residues: 439 loop : -2.41 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 484 TYR 0.020 0.001 TYR D 643 PHE 0.014 0.001 PHE C 657 TRP 0.018 0.001 TRP B 602 HIS 0.005 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00391 (31036) covalent geometry : angle 0.67904 (42080) hydrogen bonds : bond 0.04272 ( 1266) hydrogen bonds : angle 5.37209 ( 3672) *********************** 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 346 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6579 (mm-30) REVERT: A 507 TRP cc_start: 0.6036 (t60) cc_final: 0.5747 (t60) REVERT: A 635 GLU cc_start: 0.8863 (tp30) cc_final: 0.8659 (mm-30) REVERT: B 230 MET cc_start: 0.3519 (mtt) cc_final: 0.3107 (mmp) REVERT: B 496 MET cc_start: 0.8129 (tpp) cc_final: 0.7809 (tpp) REVERT: B 635 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: B 694 ARG cc_start: 0.7108 (mmt180) cc_final: 0.6815 (mmm160) REVERT: C 262 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7430 (t) REVERT: C 378 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.8117 (ttt-90) REVERT: C 625 LEU cc_start: 0.8308 (mt) cc_final: 0.8039 (mt) REVERT: D 229 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6747 (tt0) REVERT: D 390 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7581 (mt) REVERT: E 85 MET cc_start: 0.4658 (mpp) cc_final: 0.3824 (mpp) REVERT: E 372 MET cc_start: 0.8163 (mmm) cc_final: 0.7832 (mmm) REVERT: E 496 MET cc_start: 0.7085 (mmm) cc_final: 0.6885 (mmm) REVERT: E 631 GLU cc_start: 0.7621 (tp30) cc_final: 0.6843 (tp30) REVERT: E 635 GLU cc_start: 0.8415 (pm20) cc_final: 0.7998 (mm-30) outliers start: 55 outliers final: 34 residues processed: 325 average time/residue: 0.1817 time to fit residues: 99.0436 Evaluate side-chains 300 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 348 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 351 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 377 HIS ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.206435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.146789 restraints weight = 61590.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.144537 restraints weight = 42429.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.144780 restraints weight = 28165.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.145200 restraints weight = 24488.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.145573 restraints weight = 22504.902| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 31036 Z= 0.339 Angle : 0.869 12.655 42080 Z= 0.430 Chirality : 0.051 0.296 4786 Planarity : 0.007 0.076 5464 Dihedral : 7.784 140.930 4299 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.69 % Favored : 89.21 % Rotamer: Outliers : 3.08 % Allowed : 12.85 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3855 helix: -0.45 (0.12), residues: 1676 sheet: -2.58 (0.24), residues: 406 loop : -2.60 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 391 TYR 0.025 0.002 TYR D 493 PHE 0.026 0.002 PHE E 557 TRP 0.020 0.002 TRP B 298 HIS 0.009 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00787 (31036) covalent geometry : angle 0.86874 (42080) hydrogen bonds : bond 0.04831 ( 1266) hydrogen bonds : angle 5.77501 ( 3672) *********************** 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 373 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 273 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: A 507 TRP cc_start: 0.6240 (t60) cc_final: 0.6032 (t60) REVERT: B 75 MET cc_start: -0.0475 (mmm) cc_final: -0.0688 (mmm) REVERT: B 276 MET cc_start: 0.7969 (pmm) cc_final: 0.7626 (pmm) REVERT: B 490 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 496 MET cc_start: 0.8162 (tpp) cc_final: 0.7871 (tpp) REVERT: B 635 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: B 754 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7396 (mt) REVERT: C 325 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7634 (t) REVERT: C 494 THR cc_start: 0.7983 (p) cc_final: 0.7781 (p) REVERT: C 625 LEU cc_start: 0.8420 (mt) cc_final: 0.8156 (mt) REVERT: D 229 GLN cc_start: 0.7113 (tp-100) cc_final: 0.6719 (tt0) REVERT: D 390 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7696 (mp) REVERT: D 426 LYS cc_start: 0.8534 (mppt) cc_final: 0.8222 (tttt) REVERT: D 631 GLU cc_start: 0.7134 (tp30) cc_final: 0.6599 (tp30) REVERT: D 635 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6170 (mm-30) REVERT: E 85 MET cc_start: 0.4753 (mpp) cc_final: 0.4060 (mpp) REVERT: E 258 MET cc_start: 0.3686 (tpp) cc_final: 0.3396 (tpp) REVERT: E 496 MET cc_start: 0.7116 (mmm) cc_final: 0.6886 (mmm) REVERT: E 631 GLU cc_start: 0.7533 (tp30) cc_final: 0.7118 (tp30) REVERT: E 635 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: E 702 MET cc_start: 0.2995 (ptm) cc_final: 0.2741 (ptt) outliers start: 100 outliers final: 71 residues processed: 343 average time/residue: 0.1797 time to fit residues: 104.7220 Evaluate side-chains 331 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 253 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 349 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 123 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 454 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.212543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.152959 restraints weight = 63008.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154662 restraints weight = 42931.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155336 restraints weight = 25312.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.155241 restraints weight = 23321.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155903 restraints weight = 20489.084| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31036 Z= 0.135 Angle : 0.663 9.196 42080 Z= 0.327 Chirality : 0.044 0.304 4786 Planarity : 0.005 0.075 5464 Dihedral : 7.181 133.609 4299 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 2.13 % Allowed : 14.64 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3855 helix: -0.01 (0.13), residues: 1676 sheet: -2.52 (0.23), residues: 462 loop : -2.29 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 693 TYR 0.016 0.001 TYR B 493 PHE 0.019 0.001 PHE E 557 TRP 0.022 0.001 TRP B 602 HIS 0.006 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00304 (31036) covalent geometry : angle 0.66293 (42080) hydrogen bonds : bond 0.03917 ( 1266) hydrogen bonds : angle 5.16679 ( 3672) *********************** 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 372 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: A 331 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 230 MET cc_start: 0.3552 (mtt) cc_final: 0.3113 (mmp) REVERT: B 276 MET cc_start: 0.7839 (pmm) cc_final: 0.7431 (pmm) REVERT: B 496 MET cc_start: 0.8125 (tpp) cc_final: 0.7807 (tpp) REVERT: B 635 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: C 262 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7437 (t) REVERT: C 378 ARG cc_start: 0.8280 (tmm-80) cc_final: 0.7993 (ttt-90) REVERT: C 568 THR cc_start: 0.8626 (m) cc_final: 0.8243 (p) REVERT: C 625 LEU cc_start: 0.8205 (mt) cc_final: 0.7959 (mt) REVERT: D 229 GLN cc_start: 0.6950 (tp-100) cc_final: 0.6671 (tt0) REVERT: D 234 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7962 (mp10) REVERT: D 390 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7666 (mt) REVERT: D 426 LYS cc_start: 0.8388 (mppt) cc_final: 0.8032 (tttt) REVERT: D 516 MET cc_start: 0.7965 (mmm) cc_final: 0.7737 (mmm) REVERT: E 85 MET cc_start: 0.4736 (mpp) cc_final: 0.3755 (mpp) REVERT: E 372 MET cc_start: 0.7383 (mmt) cc_final: 0.7145 (mmm) REVERT: E 485 MET cc_start: 0.6768 (tpp) cc_final: 0.6512 (tpp) REVERT: E 496 MET cc_start: 0.7170 (mmm) cc_final: 0.6957 (mmm) REVERT: E 546 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6990 (tt0) REVERT: E 631 GLU cc_start: 0.7633 (tp30) cc_final: 0.7219 (tp30) REVERT: E 635 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: E 702 MET cc_start: 0.2753 (ptm) cc_final: 0.2473 (ptt) REVERT: E 713 MET cc_start: 0.7811 (ttp) cc_final: 0.7578 (mtm) outliers start: 69 outliers final: 35 residues processed: 357 average time/residue: 0.1778 time to fit residues: 107.7453 Evaluate side-chains 315 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 283 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 342 optimal weight: 0.0770 chunk 210 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 237 optimal weight: 50.0000 chunk 351 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.214129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.156010 restraints weight = 63147.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.156156 restraints weight = 43440.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.156885 restraints weight = 28010.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.157624 restraints weight = 24118.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.157646 restraints weight = 23093.935| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31036 Z= 0.117 Angle : 0.644 10.307 42080 Z= 0.315 Chirality : 0.044 0.312 4786 Planarity : 0.005 0.074 5464 Dihedral : 6.714 115.481 4299 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 2.06 % Allowed : 15.29 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3855 helix: 0.22 (0.13), residues: 1677 sheet: -2.30 (0.23), residues: 466 loop : -2.17 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 512 TYR 0.017 0.001 TYR C 224 PHE 0.023 0.001 PHE E 557 TRP 0.013 0.001 TRP A 298 HIS 0.039 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00260 (31036) covalent geometry : angle 0.64425 (42080) hydrogen bonds : bond 0.03668 ( 1266) hydrogen bonds : angle 4.93340 ( 3672) *********************** 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 375 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: A 331 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 404 LYS cc_start: 0.8813 (mptt) cc_final: 0.8484 (mmtm) REVERT: A 484 ARG cc_start: 0.7389 (mtt90) cc_final: 0.6806 (mmp-170) REVERT: A 505 TYR cc_start: 0.6675 (m-80) cc_final: 0.5778 (m-80) REVERT: A 507 TRP cc_start: 0.5996 (t60) cc_final: 0.5708 (t60) REVERT: B 83 GLN cc_start: 0.2189 (OUTLIER) cc_final: 0.1952 (tm-30) REVERT: B 230 MET cc_start: 0.3563 (mtt) cc_final: 0.3272 (mmp) REVERT: B 276 MET cc_start: 0.7759 (pmm) cc_final: 0.7297 (pmm) REVERT: B 496 MET cc_start: 0.8058 (tpp) cc_final: 0.7832 (tpp) REVERT: B 624 SER cc_start: 0.8404 (t) cc_final: 0.7929 (p) REVERT: B 754 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7124 (mt) REVERT: C 378 ARG cc_start: 0.8212 (tmm-80) cc_final: 0.7952 (ttt-90) REVERT: C 568 THR cc_start: 0.8548 (m) cc_final: 0.8136 (p) REVERT: C 625 LEU cc_start: 0.8023 (mt) cc_final: 0.7786 (mt) REVERT: D 229 GLN cc_start: 0.6899 (tp-100) cc_final: 0.6663 (tt0) REVERT: D 234 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8013 (mp10) REVERT: D 426 LYS cc_start: 0.8307 (mppt) cc_final: 0.7959 (tttt) REVERT: E 85 MET cc_start: 0.4643 (mpp) cc_final: 0.4038 (mpp) REVERT: E 258 MET cc_start: 0.3674 (tpp) cc_final: 0.3472 (tpp) REVERT: E 496 MET cc_start: 0.7254 (mmm) cc_final: 0.7023 (mmm) REVERT: E 631 GLU cc_start: 0.7656 (tp30) cc_final: 0.7217 (tp30) REVERT: E 635 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: E 702 MET cc_start: 0.2785 (ptm) cc_final: 0.2470 (ptt) outliers start: 67 outliers final: 38 residues processed: 356 average time/residue: 0.1794 time to fit residues: 107.8361 Evaluate side-chains 326 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 93 optimal weight: 50.0000 chunk 311 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 6 optimal weight: 50.0000 chunk 120 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** 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 = 0.4787 r_free = 0.4787 target = 0.211919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.151349 restraints weight = 62315.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.151996 restraints weight = 38619.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.152633 restraints weight = 26178.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.153150 restraints weight = 21206.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153451 restraints weight = 19192.012| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31036 Z= 0.160 Angle : 0.671 9.346 42080 Z= 0.328 Chirality : 0.045 0.301 4786 Planarity : 0.005 0.076 5464 Dihedral : 6.623 120.321 4299 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 2.28 % Allowed : 15.90 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3855 helix: 0.23 (0.13), residues: 1684 sheet: -2.30 (0.24), residues: 451 loop : -2.18 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 378 TYR 0.021 0.001 TYR D 225 PHE 0.030 0.001 PHE E 557 TRP 0.016 0.001 TRP A 431 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00372 (31036) covalent geometry : angle 0.67126 (42080) hydrogen bonds : bond 0.03774 ( 1266) hydrogen bonds : angle 4.98819 ( 3672) *********************** 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 351 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.4748 (tt0) cc_final: 0.4105 (tm-30) REVERT: A 247 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6575 (mm-30) REVERT: A 331 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 484 ARG cc_start: 0.7470 (mtt90) cc_final: 0.6854 (mmp-170) REVERT: A 505 TYR cc_start: 0.6725 (m-80) cc_final: 0.5812 (m-80) REVERT: A 698 MET cc_start: 0.2971 (mtp) cc_final: 0.2684 (tpp) REVERT: B 83 GLN cc_start: 0.2078 (OUTLIER) cc_final: 0.1813 (tm-30) REVERT: B 230 MET cc_start: 0.3571 (mtt) cc_final: 0.3152 (mmp) REVERT: B 276 MET cc_start: 0.7797 (pmm) cc_final: 0.7473 (pmm) REVERT: B 496 MET cc_start: 0.8139 (tpp) cc_final: 0.7896 (tpp) REVERT: B 754 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7361 (mt) REVERT: C 625 LEU cc_start: 0.8140 (mt) cc_final: 0.7917 (mt) REVERT: D 217 MET cc_start: 0.5882 (tmm) cc_final: 0.5592 (ttp) REVERT: D 234 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8086 (mp10) REVERT: D 276 MET cc_start: 0.4479 (tmm) cc_final: 0.3962 (tmm) REVERT: D 426 LYS cc_start: 0.8382 (mppt) cc_final: 0.8026 (tttt) REVERT: E 85 MET cc_start: 0.4790 (mpp) cc_final: 0.4012 (mpp) REVERT: E 258 MET cc_start: 0.3655 (tpp) cc_final: 0.3448 (tpp) REVERT: E 496 MET cc_start: 0.7216 (mmm) cc_final: 0.6987 (mmm) REVERT: E 631 GLU cc_start: 0.7654 (tp30) cc_final: 0.7226 (tp30) REVERT: E 635 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: E 702 MET cc_start: 0.2868 (ptm) cc_final: 0.2576 (ptt) outliers start: 74 outliers final: 52 residues processed: 330 average time/residue: 0.1740 time to fit residues: 97.5508 Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 33 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 172 optimal weight: 40.0000 chunk 151 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 226 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN E 664 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.213596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154994 restraints weight = 62985.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.155746 restraints weight = 41394.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.155885 restraints weight = 25485.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156173 restraints weight = 22053.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.156389 restraints weight = 20624.419| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31036 Z= 0.127 Angle : 0.655 15.330 42080 Z= 0.315 Chirality : 0.044 0.300 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.426 121.544 4299 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 2.10 % Allowed : 16.39 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3855 helix: 0.34 (0.13), residues: 1680 sheet: -2.28 (0.23), residues: 461 loop : -2.14 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 378 TYR 0.018 0.001 TYR D 643 PHE 0.027 0.001 PHE E 557 TRP 0.016 0.001 TRP A 563 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00290 (31036) covalent geometry : angle 0.65503 (42080) hydrogen bonds : bond 0.03618 ( 1266) hydrogen bonds : angle 4.85092 ( 3672) *********************** 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 351 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 283 time to evaluate : 1.182 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 247 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: A 331 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 404 LYS cc_start: 0.8800 (mptt) cc_final: 0.8550 (ttpt) REVERT: A 484 ARG cc_start: 0.7408 (mtt90) cc_final: 0.6809 (mmp-170) REVERT: A 505 TYR cc_start: 0.6665 (m-80) cc_final: 0.5816 (m-80) REVERT: A 698 MET cc_start: 0.3059 (mtp) cc_final: 0.2781 (tpp) REVERT: B 83 GLN cc_start: 0.2092 (OUTLIER) cc_final: 0.1859 (tm-30) REVERT: B 230 MET cc_start: 0.3475 (mtt) cc_final: 0.3081 (mmp) REVERT: B 276 MET cc_start: 0.7737 (pmm) cc_final: 0.7405 (pmm) REVERT: B 496 MET cc_start: 0.8122 (tpp) cc_final: 0.7878 (tpp) REVERT: B 624 SER cc_start: 0.8378 (t) cc_final: 0.7898 (p) REVERT: B 754 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7242 (mt) REVERT: C 378 ARG cc_start: 0.8290 (tmm-80) cc_final: 0.7972 (ttt-90) REVERT: D 217 MET cc_start: 0.5888 (tmm) cc_final: 0.5580 (ttp) REVERT: D 234 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8057 (mp10) REVERT: D 276 MET cc_start: 0.4546 (tmm) cc_final: 0.4115 (tmm) REVERT: D 426 LYS cc_start: 0.8311 (mppt) cc_final: 0.7962 (tttt) REVERT: D 768 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: E 276 MET cc_start: -0.2359 (OUTLIER) cc_final: -0.3186 (tpt) REVERT: E 496 MET cc_start: 0.7271 (mmm) cc_final: 0.7051 (mmm) REVERT: E 631 GLU cc_start: 0.7627 (tp30) cc_final: 0.7190 (tp30) REVERT: E 635 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: E 702 MET cc_start: 0.2818 (ptm) cc_final: 0.2539 (ptt) REVERT: E 731 HIS cc_start: 0.4724 (OUTLIER) cc_final: 0.4122 (p-80) outliers start: 68 outliers final: 48 residues processed: 333 average time/residue: 0.1747 time to fit residues: 98.1569 Evaluate side-chains 330 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 493 TYR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 731 HIS Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 109 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 379 optimal weight: 0.0470 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 229 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.213431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154102 restraints weight = 62825.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155813 restraints weight = 44417.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.155729 restraints weight = 28510.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156117 restraints weight = 24763.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.156468 restraints weight = 22787.933| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31036 Z= 0.131 Angle : 0.660 11.918 42080 Z= 0.318 Chirality : 0.044 0.280 4786 Planarity : 0.005 0.080 5464 Dihedral : 6.316 124.441 4299 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 2.22 % Allowed : 16.36 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3855 helix: 0.42 (0.13), residues: 1677 sheet: -2.22 (0.24), residues: 451 loop : -2.07 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 479 TYR 0.026 0.001 TYR D 225 PHE 0.026 0.001 PHE E 557 TRP 0.020 0.001 TRP A 507 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00302 (31036) covalent geometry : angle 0.66028 (42080) hydrogen bonds : bond 0.03615 ( 1266) hydrogen bonds : angle 4.81641 ( 3672) *********************** 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 350 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 1.291 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 247 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: A 331 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 404 LYS cc_start: 0.8777 (mptt) cc_final: 0.8563 (ttpt) REVERT: A 484 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6803 (mmp-170) REVERT: A 505 TYR cc_start: 0.6560 (m-80) cc_final: 0.5793 (m-80) REVERT: A 698 MET cc_start: 0.3026 (mtp) cc_final: 0.2825 (tpp) REVERT: B 83 GLN cc_start: 0.1977 (OUTLIER) cc_final: 0.1746 (tm-30) REVERT: B 230 MET cc_start: 0.3473 (mtt) cc_final: 0.3151 (mmp) REVERT: B 276 MET cc_start: 0.7758 (pmm) cc_final: 0.7467 (pmm) REVERT: B 624 SER cc_start: 0.8366 (t) cc_final: 0.7912 (p) REVERT: B 754 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7152 (mt) REVERT: C 378 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.8013 (ttt-90) REVERT: D 217 MET cc_start: 0.6054 (tmm) cc_final: 0.5726 (ttp) REVERT: D 262 VAL cc_start: 0.7321 (t) cc_final: 0.7094 (t) REVERT: D 276 MET cc_start: 0.4598 (tmm) cc_final: 0.4051 (tmm) REVERT: D 426 LYS cc_start: 0.8351 (mppt) cc_final: 0.7999 (tttt) REVERT: D 768 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5843 (m-80) REVERT: E 75 MET cc_start: 0.1746 (ptp) cc_final: 0.1481 (ptp) REVERT: E 258 MET cc_start: 0.3261 (tpp) cc_final: 0.2816 (tpp) REVERT: E 276 MET cc_start: -0.2383 (OUTLIER) cc_final: -0.3199 (tpt) REVERT: E 496 MET cc_start: 0.7314 (mmm) cc_final: 0.7048 (mmm) REVERT: E 631 GLU cc_start: 0.7742 (tp30) cc_final: 0.7259 (tp30) REVERT: E 635 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: E 731 HIS cc_start: 0.4659 (OUTLIER) cc_final: 0.4070 (p-80) outliers start: 72 outliers final: 54 residues processed: 330 average time/residue: 0.1771 time to fit residues: 99.3279 Evaluate side-chains 335 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 731 HIS Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 254 optimal weight: 10.0000 chunk 278 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 338 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 321 optimal weight: 40.0000 chunk 124 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** 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 = 0.4784 r_free = 0.4784 target = 0.211618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.153062 restraints weight = 62621.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150886 restraints weight = 40018.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.152184 restraints weight = 32639.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152901 restraints weight = 23042.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153182 restraints weight = 21339.190| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31036 Z= 0.175 Angle : 0.703 12.047 42080 Z= 0.340 Chirality : 0.045 0.271 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.396 125.642 4299 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.12 % Favored : 91.80 % Rotamer: Outliers : 1.97 % Allowed : 16.73 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3855 helix: 0.34 (0.13), residues: 1681 sheet: -2.23 (0.24), residues: 451 loop : -2.12 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 378 TYR 0.020 0.001 TYR D 643 PHE 0.027 0.001 PHE E 557 TRP 0.024 0.001 TRP A 507 HIS 0.010 0.001 HIS E 664 Details of bonding type rmsd covalent geometry : bond 0.00409 (31036) covalent geometry : angle 0.70266 (42080) hydrogen bonds : bond 0.03784 ( 1266) hydrogen bonds : angle 4.91006 ( 3672) ********************** 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 339 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.4686 (tt0) cc_final: 0.4000 (tm-30) REVERT: A 247 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: A 331 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: A 401 MET cc_start: 0.7841 (mtt) cc_final: 0.6909 (mmp) REVERT: A 484 ARG cc_start: 0.7379 (mtt90) cc_final: 0.6789 (mmp-170) REVERT: A 505 TYR cc_start: 0.6734 (m-80) cc_final: 0.5891 (m-80) REVERT: B 83 GLN cc_start: 0.2046 (OUTLIER) cc_final: 0.1801 (tm-30) REVERT: B 230 MET cc_start: 0.3603 (mtt) cc_final: 0.3297 (mmp) REVERT: B 276 MET cc_start: 0.7778 (pmm) cc_final: 0.7535 (pmm) REVERT: B 754 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7385 (mt) REVERT: C 378 ARG cc_start: 0.8324 (tmm-80) cc_final: 0.8030 (ttt-90) REVERT: D 217 MET cc_start: 0.5969 (tmm) cc_final: 0.5624 (ttp) REVERT: D 258 MET cc_start: 0.5011 (mtt) cc_final: 0.4744 (mtp) REVERT: D 276 MET cc_start: 0.4656 (tmm) cc_final: 0.4310 (tmm) REVERT: D 426 LYS cc_start: 0.8356 (mppt) cc_final: 0.7969 (tttt) REVERT: D 768 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: E 76 ARG cc_start: 0.3065 (tpt170) cc_final: 0.2811 (tpm170) REVERT: E 85 MET cc_start: 0.4731 (mpp) cc_final: 0.3973 (mpp) REVERT: E 258 MET cc_start: 0.3112 (tpp) cc_final: 0.2687 (tpp) REVERT: E 276 MET cc_start: -0.2275 (OUTLIER) cc_final: -0.3180 (tpt) REVERT: E 496 MET cc_start: 0.7286 (mmm) cc_final: 0.7055 (mmm) REVERT: E 631 GLU cc_start: 0.7705 (tp30) cc_final: 0.7236 (tp30) REVERT: E 635 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: E 731 HIS cc_start: 0.4712 (OUTLIER) cc_final: 0.4126 (p-80) outliers start: 64 outliers final: 53 residues processed: 322 average time/residue: 0.1837 time to fit residues: 99.8537 Evaluate side-chains 330 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 731 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 262 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 368 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.213020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153824 restraints weight = 62977.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.155699 restraints weight = 38214.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.156092 restraints weight = 24316.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.156740 restraints weight = 22404.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.156861 restraints weight = 18433.952| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31036 Z= 0.130 Angle : 0.663 12.144 42080 Z= 0.319 Chirality : 0.044 0.257 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.242 124.731 4299 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 2.00 % Allowed : 16.86 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3855 helix: 0.45 (0.13), residues: 1682 sheet: -2.22 (0.24), residues: 457 loop : -2.02 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.028 0.001 TYR D 225 PHE 0.025 0.001 PHE E 557 TRP 0.028 0.001 TRP A 507 HIS 0.005 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00300 (31036) covalent geometry : angle 0.66273 (42080) hydrogen bonds : bond 0.03561 ( 1266) hydrogen bonds : angle 4.75902 ( 3672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6645.50 seconds wall clock time: 115 minutes 11.94 seconds (6911.94 seconds total)