Starting phenix.real_space_refine on Thu Jun 26 08:44:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuw_34113/06_2025/7yuw_34113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuw_34113/06_2025/7yuw_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_34113/06_2025/7yuw_34113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuw_34113/06_2025/7yuw_34113.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuw_34113/06_2025/7yuw_34113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuw_34113/06_2025/7yuw_34113.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.64s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.62, per 1000 atoms: 0.55 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: 6.83 Conformation dependent library (CDL) restraints added in 3.6 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: 3.41 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: 10.33 Time building geometry restraints manager: 8.16 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 62.000 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.620 ------------------------------------------------------------------------------- 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 : 16.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (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 TRP 0.033 0.002 TRP B 292 HIS 0.005 0.001 HIS E 377 PHE 0.011 0.001 PHE E 557 TYR 0.022 0.001 TYR A 493 ARG 0.008 0.000 ARG E 529 Details of bonding type rmsd hydrogen bonds : bond 0.16841 ( 1266) hydrogen bonds : angle 6.84997 ( 3672) covalent geometry : bond 0.00381 (31036) covalent geometry : angle 0.76370 (42080) *********************** 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 : 3.559 Fit side-chains revert: symmetry clash 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: 0.2830 (p90) REVERT: B 85 MET cc_start: 0.4867 (mmt) cc_final: 0.4461 (mmt) REVERT: B 488 ILE cc_start: 0.7868 (mm) cc_final: 0.7378 (mt) REVERT: C 378 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.7867 (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: 0.3825 time to fit residues: 226.2086 Evaluate side-chains 270 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 325 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 0.0670 chunk 155 optimal weight: 30.0000 chunk 301 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 349 optimal weight: 10.0000 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** 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 739 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.212344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154189 restraints weight = 62023.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.154011 restraints weight = 39940.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154220 restraints weight = 27045.856| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31036 Z= 0.178 Angle : 0.697 8.505 42080 Z= 0.348 Chirality : 0.046 0.279 4786 Planarity : 0.006 0.064 5464 Dihedral : 7.565 172.950 4301 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.38 % Favored : 91.52 % Rotamer: Outliers : 0.99 % Allowed : 7.30 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 3855 helix: -0.01 (0.13), residues: 1699 sheet: -2.39 (0.23), residues: 434 loop : -2.42 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 298 HIS 0.005 0.001 HIS E 377 PHE 0.020 0.002 PHE C 657 TYR 0.037 0.002 TYR C 768 ARG 0.007 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 1266) hydrogen bonds : angle 5.53594 ( 3672) covalent geometry : bond 0.00399 (31036) covalent geometry : angle 0.69694 (42080) *********************** 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 332 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.2538 (p90) cc_final: 0.2025 (p90) REVERT: B 85 MET cc_start: 0.5132 (mmt) cc_final: 0.4916 (mmt) REVERT: B 432 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7779 (mtm180) REVERT: B 484 ARG cc_start: 0.7126 (mtm-85) cc_final: 0.6816 (mtp85) REVERT: B 488 ILE cc_start: 0.8031 (mm) cc_final: 0.7526 (mt) REVERT: C 160 MET cc_start: 0.4269 (tmm) cc_final: 0.4068 (mpp) REVERT: C 230 MET cc_start: 0.8420 (tmm) cc_final: 0.8131 (tmm) REVERT: C 378 ARG cc_start: 0.8246 (tmm-80) cc_final: 0.8033 (ttt-90) REVERT: C 625 LEU cc_start: 0.8149 (mt) cc_final: 0.7885 (mt) REVERT: E 85 MET cc_start: 0.4910 (mpp) cc_final: 0.3912 (mpp) REVERT: E 496 MET cc_start: 0.7150 (mmm) cc_final: 0.6909 (mmm) REVERT: E 631 GLU cc_start: 0.7393 (tp30) cc_final: 0.6600 (tp30) REVERT: E 635 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8046 (mm-30) outliers start: 32 outliers final: 17 residues processed: 315 average time/residue: 0.3866 time to fit residues: 201.8636 Evaluate side-chains 282 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 613 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 324 ASP 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 769 LEU Chi-restraints excluded: chain D residue 414 VAL 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 E residue 431 TRP Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 664 HIS 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 117 optimal weight: 7.9990 chunk 334 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 313 optimal weight: 0.6980 chunk 345 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 217 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.210551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.151528 restraints weight = 61033.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.151730 restraints weight = 38796.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151606 restraints weight = 25870.451| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31036 Z= 0.203 Angle : 0.708 9.334 42080 Z= 0.351 Chirality : 0.046 0.281 4786 Planarity : 0.005 0.062 5464 Dihedral : 7.404 156.284 4299 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 1.76 % Allowed : 9.89 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3855 helix: -0.03 (0.13), residues: 1684 sheet: -2.45 (0.23), residues: 451 loop : -2.41 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 431 HIS 0.006 0.001 HIS C 454 PHE 0.015 0.002 PHE C 657 TYR 0.029 0.002 TYR B 289 ARG 0.008 0.000 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1266) hydrogen bonds : angle 5.39330 ( 3672) covalent geometry : bond 0.00467 (31036) covalent geometry : angle 0.70776 (42080) *********************** 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 340 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8856 (pm20) REVERT: A 247 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6489 (mm-30) REVERT: A 507 TRP cc_start: 0.6023 (t60) cc_final: 0.5733 (t60) REVERT: B 230 MET cc_start: 0.3388 (mtt) cc_final: 0.2907 (mmp) REVERT: B 757 LYS cc_start: 0.6360 (mtmt) cc_final: 0.6134 (ttpt) REVERT: C 262 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7585 (t) REVERT: C 625 LEU cc_start: 0.8241 (mt) cc_final: 0.7971 (mt) REVERT: D 229 GLN cc_start: 0.7125 (tp-100) cc_final: 0.6681 (tt0) REVERT: D 325 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7416 (t) REVERT: D 390 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7656 (mt) REVERT: D 426 LYS cc_start: 0.8442 (mppt) cc_final: 0.8178 (tttt) REVERT: E 85 MET cc_start: 0.4953 (mpp) cc_final: 0.3946 (mpp) REVERT: E 258 MET cc_start: 0.3650 (tpp) cc_final: 0.3448 (tpp) REVERT: E 265 LYS cc_start: 0.3553 (pttt) cc_final: 0.2954 (mtpp) REVERT: E 631 GLU cc_start: 0.7405 (tp30) cc_final: 0.6568 (tp30) REVERT: E 635 GLU cc_start: 0.8320 (pm20) cc_final: 0.7976 (mm-30) outliers start: 57 outliers final: 34 residues processed: 322 average time/residue: 0.3790 time to fit residues: 204.2879 Evaluate side-chains 306 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 3.108 ------------------------------------------------------------------------------- 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 574 ILE Chi-restraints excluded: chain B residue 335 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 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 758 LEU 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 523 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 325 VAL 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 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR 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 251 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 227 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.210896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.150956 restraints weight = 61278.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.150021 restraints weight = 37564.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.151624 restraints weight = 27753.081| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31036 Z= 0.180 Angle : 0.679 8.730 42080 Z= 0.335 Chirality : 0.045 0.296 4786 Planarity : 0.005 0.067 5464 Dihedral : 7.207 142.174 4299 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.61 % Favored : 91.31 % Rotamer: Outliers : 2.00 % Allowed : 11.77 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3855 helix: 0.02 (0.13), residues: 1685 sheet: -2.38 (0.23), residues: 441 loop : -2.34 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 431 HIS 0.005 0.001 HIS A 377 PHE 0.023 0.001 PHE E 557 TYR 0.019 0.001 TYR D 643 ARG 0.005 0.000 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 1266) hydrogen bonds : angle 5.24188 ( 3672) covalent geometry : bond 0.00412 (31036) covalent geometry : angle 0.67911 (42080) *********************** 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 363 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 298 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: A 507 TRP cc_start: 0.6107 (t60) cc_final: 0.5821 (t60) REVERT: B 230 MET cc_start: 0.3549 (mtt) cc_final: 0.3092 (mmp) REVERT: B 635 GLU cc_start: 0.7598 (pm20) cc_final: 0.7340 (pm20) REVERT: B 757 LYS cc_start: 0.6419 (mtmt) cc_final: 0.6163 (ttpt) REVERT: C 262 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7551 (t) REVERT: C 439 MET cc_start: 0.7911 (mmm) cc_final: 0.7669 (mmm) REVERT: C 625 LEU cc_start: 0.8203 (mt) cc_final: 0.7948 (mt) REVERT: D 229 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6678 (tt0) REVERT: D 426 LYS cc_start: 0.8434 (mppt) cc_final: 0.8152 (tttt) REVERT: E 85 MET cc_start: 0.4740 (mpp) cc_final: 0.3919 (mpp) REVERT: E 265 LYS cc_start: 0.3503 (pttt) cc_final: 0.2802 (mmmt) REVERT: E 546 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7005 (tt0) REVERT: E 631 GLU cc_start: 0.7512 (tp30) cc_final: 0.6826 (tp30) REVERT: E 635 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8093 (mm-30) outliers start: 65 outliers final: 43 residues processed: 345 average time/residue: 0.3752 time to fit residues: 218.5003 Evaluate side-chains 322 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 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 305 VAL Chi-restraints excluded: chain B residue 335 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 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 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 470 THR 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 681 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 38 MET Chi-restraints excluded: chain D residue 290 LEU 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 528 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE 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 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 22 optimal weight: 9.9990 chunk 368 optimal weight: 30.0000 chunk 343 optimal weight: 0.8980 chunk 331 optimal weight: 40.0000 chunk 133 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 281 optimal weight: 1.9990 chunk 240 optimal weight: 30.0000 chunk 221 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 A 475 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** 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** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.206778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.147561 restraints weight = 60856.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.143603 restraints weight = 45876.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.145598 restraints weight = 34076.152| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 31036 Z= 0.303 Angle : 0.822 11.352 42080 Z= 0.406 Chirality : 0.050 0.317 4786 Planarity : 0.006 0.072 5464 Dihedral : 7.493 130.244 4299 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.19 % Favored : 89.73 % Rotamer: Outliers : 3.17 % Allowed : 13.04 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 3855 helix: -0.27 (0.13), residues: 1682 sheet: -2.45 (0.24), residues: 418 loop : -2.47 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 298 HIS 0.008 0.002 HIS D 454 PHE 0.036 0.002 PHE E 557 TYR 0.023 0.002 TYR D 643 ARG 0.006 0.001 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 1266) hydrogen bonds : angle 5.56721 ( 3672) covalent geometry : bond 0.00703 (31036) covalent geometry : angle 0.82232 (42080) *********************** 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 382 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 279 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: A 331 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 507 TRP cc_start: 0.6255 (t60) cc_final: 0.6015 (t60) REVERT: B 276 MET cc_start: 0.7923 (pmm) cc_final: 0.7570 (pmm) REVERT: B 635 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: B 754 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7446 (mt) REVERT: C 625 LEU cc_start: 0.8412 (mt) cc_final: 0.8123 (mt) REVERT: D 229 GLN cc_start: 0.6963 (tp-100) cc_final: 0.6664 (tt0) REVERT: D 234 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7998 (mp10) REVERT: D 390 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7768 (mt) REVERT: D 426 LYS cc_start: 0.8486 (mppt) cc_final: 0.8180 (tttt) REVERT: E 85 MET cc_start: 0.4708 (mpp) cc_final: 0.4038 (mpp) REVERT: E 258 MET cc_start: 0.3521 (tpp) cc_final: 0.3264 (tpp) REVERT: E 265 LYS cc_start: 0.3590 (pttt) cc_final: 0.2982 (mtpp) REVERT: E 546 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6882 (tt0) REVERT: E 631 GLU cc_start: 0.7568 (tp30) cc_final: 0.7115 (tp30) REVERT: E 635 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: E 713 MET cc_start: 0.7876 (ttp) cc_final: 0.7648 (mtm) outliers start: 103 outliers final: 70 residues processed: 355 average time/residue: 0.3860 time to fit residues: 230.5718 Evaluate side-chains 337 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 261 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 574 ILE 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 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 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 681 ILE 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 B residue 769 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 379 ILE 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 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 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 443 LEU 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 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 D residue 749 GLU Chi-restraints excluded: chain E residue 20 THR 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 715 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 279 optimal weight: 0.7980 chunk 377 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 265 optimal weight: 0.0050 chunk 123 optimal weight: 1.9990 chunk 317 optimal weight: 50.0000 chunk 315 optimal weight: 20.0000 chunk 304 optimal weight: 0.5980 chunk 333 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 454 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 177 GLN E 659 ASN ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.211881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153707 restraints weight = 61290.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.153008 restraints weight = 42466.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.153652 restraints weight = 26353.745| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31036 Z= 0.138 Angle : 0.667 9.756 42080 Z= 0.327 Chirality : 0.045 0.309 4786 Planarity : 0.005 0.075 5464 Dihedral : 6.968 117.101 4299 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 2.25 % Allowed : 14.82 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3855 helix: 0.06 (0.13), residues: 1678 sheet: -2.39 (0.23), residues: 444 loop : -2.30 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 292 HIS 0.006 0.001 HIS E 377 PHE 0.027 0.001 PHE E 557 TYR 0.020 0.001 TYR C 224 ARG 0.010 0.000 ARG C 503 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 1266) hydrogen bonds : angle 5.09454 ( 3672) covalent geometry : bond 0.00311 (31036) covalent geometry : angle 0.66732 (42080) *********************** 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 373 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: A 230 MET cc_start: 0.6846 (mmp) cc_final: 0.6574 (mmp) REVERT: A 247 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6521 (mm-30) REVERT: A 296 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6638 (p) REVERT: A 331 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: B 230 MET cc_start: 0.3359 (mtt) cc_final: 0.2784 (mmp) REVERT: B 276 MET cc_start: 0.7837 (pmm) cc_final: 0.7452 (pmm) REVERT: B 566 LEU cc_start: 0.8273 (tp) cc_final: 0.7897 (tt) REVERT: B 635 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: B 754 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7222 (mt) REVERT: C 625 LEU cc_start: 0.8205 (mt) cc_final: 0.7952 (mt) REVERT: D 217 MET cc_start: 0.5949 (tmm) cc_final: 0.5600 (ttp) REVERT: D 229 GLN cc_start: 0.6893 (tp-100) cc_final: 0.6693 (tt0) REVERT: D 234 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8026 (mp10) REVERT: D 390 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7672 (mt) REVERT: D 426 LYS cc_start: 0.8380 (mppt) cc_final: 0.8010 (tttt) REVERT: D 440 LEU cc_start: 0.7624 (mt) cc_final: 0.7356 (mt) REVERT: E 85 MET cc_start: 0.4760 (mpp) cc_final: 0.3990 (mpp) REVERT: E 258 MET cc_start: 0.3566 (tpp) cc_final: 0.3347 (tpp) REVERT: E 265 LYS cc_start: 0.3580 (pttt) cc_final: 0.2919 (mmmt) REVERT: E 485 MET cc_start: 0.6722 (tpp) cc_final: 0.6481 (tpp) REVERT: E 631 GLU cc_start: 0.7569 (tp30) cc_final: 0.7151 (tp30) REVERT: E 635 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: E 698 MET cc_start: 0.3320 (mtm) cc_final: 0.2989 (mpp) REVERT: E 713 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7561 (mtm) outliers start: 73 outliers final: 40 residues processed: 352 average time/residue: 0.3716 time to fit residues: 220.3074 Evaluate side-chains 319 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 3.234 ------------------------------------------------------------------------------- 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 296 VAL 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 45 PHE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 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 B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 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 765 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 335 VAL 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 476 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain E residue 84 VAL 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 713 MET 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 182 optimal weight: 9.9990 chunk 15 optimal weight: 0.0050 chunk 96 optimal weight: 40.0000 chunk 173 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 593 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** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.212386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153165 restraints weight = 62166.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.153475 restraints weight = 40829.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154269 restraints weight = 26959.386| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31036 Z= 0.135 Angle : 0.657 9.474 42080 Z= 0.321 Chirality : 0.044 0.309 4786 Planarity : 0.005 0.077 5464 Dihedral : 6.678 118.617 4299 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 2.28 % Allowed : 15.16 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3855 helix: 0.19 (0.13), residues: 1690 sheet: -2.32 (0.23), residues: 451 loop : -2.18 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 507 HIS 0.028 0.001 HIS B 319 PHE 0.023 0.001 PHE E 557 TYR 0.016 0.001 TYR D 643 ARG 0.008 0.000 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 1266) hydrogen bonds : angle 4.97147 ( 3672) covalent geometry : bond 0.00308 (31036) covalent geometry : angle 0.65701 (42080) *********************** 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 366 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 292 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: A 240 GLU cc_start: 0.4745 (tt0) cc_final: 0.4081 (tm-30) REVERT: A 247 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: A 296 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6572 (p) REVERT: A 331 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 404 LYS cc_start: 0.8789 (mptt) cc_final: 0.8433 (mmtm) REVERT: A 505 TYR cc_start: 0.6788 (m-80) cc_final: 0.5731 (m-80) REVERT: A 507 TRP cc_start: 0.6041 (t60) cc_final: 0.5796 (t60) REVERT: B 276 MET cc_start: 0.7783 (pmm) cc_final: 0.7465 (pmm) REVERT: B 635 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: B 754 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7214 (mt) REVERT: C 625 LEU cc_start: 0.8135 (mt) cc_final: 0.7862 (mt) REVERT: D 217 MET cc_start: 0.5960 (tmm) cc_final: 0.5636 (ttp) REVERT: D 390 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7739 (mt) REVERT: D 426 LYS cc_start: 0.8305 (mppt) cc_final: 0.7951 (tttt) REVERT: D 516 MET cc_start: 0.7881 (mmm) cc_final: 0.7658 (mmm) REVERT: E 85 MET cc_start: 0.4727 (mpp) cc_final: 0.3930 (mpp) REVERT: E 265 LYS cc_start: 0.3562 (pttt) cc_final: 0.2932 (mmmt) REVERT: E 631 GLU cc_start: 0.7623 (tp30) cc_final: 0.7193 (tp30) REVERT: E 635 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: E 713 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7551 (mtm) outliers start: 74 outliers final: 47 residues processed: 346 average time/residue: 0.3742 time to fit residues: 218.5390 Evaluate side-chains 333 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 254 GLU Chi-restraints excluded: chain A residue 296 VAL 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 A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE 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 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 635 GLU 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 B residue 769 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 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 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 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 443 LEU 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 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP 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 713 MET 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 257 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 171 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 180 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 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 ** B 593 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 ** E 727 GLN ** 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 = 0.212610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152179 restraints weight = 63213.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.153545 restraints weight = 45204.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.154685 restraints weight = 29622.448| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31036 Z= 0.132 Angle : 0.656 11.088 42080 Z= 0.318 Chirality : 0.044 0.297 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.482 121.711 4299 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 93.00 % Rotamer: Outliers : 2.40 % Allowed : 15.56 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3855 helix: 0.30 (0.13), residues: 1687 sheet: -2.24 (0.24), residues: 444 loop : -2.14 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 563 HIS 0.005 0.001 HIS A 377 PHE 0.021 0.001 PHE E 557 TYR 0.024 0.001 TYR D 225 ARG 0.007 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1266) hydrogen bonds : angle 4.86654 ( 3672) covalent geometry : bond 0.00303 (31036) covalent geometry : angle 0.65609 (42080) *********************** 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 371 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 293 time to evaluate : 3.353 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 211 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: A 240 GLU cc_start: 0.4745 (tt0) cc_final: 0.4043 (tm-30) REVERT: A 247 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: A 331 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 404 LYS cc_start: 0.8761 (mptt) cc_final: 0.8462 (mmtm) REVERT: A 505 TYR cc_start: 0.6683 (m-80) cc_final: 0.5708 (m-80) REVERT: B 276 MET cc_start: 0.7720 (pmm) cc_final: 0.7454 (pmm) REVERT: B 432 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: B 635 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: B 754 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7061 (mt) REVERT: C 625 LEU cc_start: 0.8049 (mt) cc_final: 0.7794 (mt) REVERT: D 217 MET cc_start: 0.5970 (tmm) cc_final: 0.5614 (ttp) REVERT: D 390 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7742 (mt) REVERT: D 426 LYS cc_start: 0.8310 (mppt) cc_final: 0.7963 (tttt) REVERT: E 85 MET cc_start: 0.4663 (mpp) cc_final: 0.3879 (mpp) REVERT: E 258 MET cc_start: 0.3297 (tpp) cc_final: 0.3023 (tpp) REVERT: E 265 LYS cc_start: 0.3546 (pttt) cc_final: 0.2855 (mmmt) REVERT: E 276 MET cc_start: -0.2204 (OUTLIER) cc_final: -0.3082 (tpt) REVERT: E 631 GLU cc_start: 0.7624 (tp30) cc_final: 0.7162 (tp30) REVERT: E 635 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: E 713 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7566 (mtm) outliers start: 78 outliers final: 52 residues processed: 349 average time/residue: 0.3909 time to fit residues: 232.3839 Evaluate side-chains 337 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 3.177 ------------------------------------------------------------------------------- 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 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 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 45 PHE 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 422 ASP 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 635 GLU 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 B residue 769 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 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 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 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 443 LEU 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 681 ILE Chi-restraints excluded: chain D residue 703 THR 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 713 MET 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 47 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 382 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS B 73 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.212075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.150491 restraints weight = 62804.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151501 restraints weight = 41173.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153164 restraints weight = 26466.608| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31036 Z= 0.160 Angle : 0.683 12.124 42080 Z= 0.330 Chirality : 0.045 0.286 4786 Planarity : 0.005 0.081 5464 Dihedral : 6.479 123.797 4299 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 2.22 % Allowed : 16.09 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3855 helix: 0.27 (0.13), residues: 1688 sheet: -2.22 (0.24), residues: 444 loop : -2.16 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 292 HIS 0.008 0.001 HIS E 664 PHE 0.019 0.001 PHE E 557 TYR 0.019 0.001 TYR D 643 ARG 0.011 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1266) hydrogen bonds : angle 4.90854 ( 3672) covalent geometry : bond 0.00375 (31036) covalent geometry : angle 0.68302 (42080) *********************** 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 355 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 9.238 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 211 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8810 (pm20) REVERT: A 240 GLU cc_start: 0.4816 (tt0) cc_final: 0.4353 (pp20) REVERT: A 247 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: A 331 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 404 LYS cc_start: 0.8809 (mptt) cc_final: 0.8497 (mmtm) REVERT: A 505 TYR cc_start: 0.6831 (m-80) cc_final: 0.5883 (m-80) REVERT: A 635 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8158 (pp20) REVERT: A 698 MET cc_start: 0.3001 (mtp) cc_final: 0.2679 (ttm) REVERT: B 230 MET cc_start: 0.3373 (mtt) cc_final: 0.2979 (mmp) REVERT: B 276 MET cc_start: 0.7800 (pmm) cc_final: 0.7558 (pmm) REVERT: B 432 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7733 (mtm-85) REVERT: B 635 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: B 754 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7231 (mt) REVERT: C 625 LEU cc_start: 0.8148 (mt) cc_final: 0.7867 (mt) REVERT: D 217 MET cc_start: 0.6003 (tmm) cc_final: 0.5691 (ttp) REVERT: D 390 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7634 (mt) REVERT: D 426 LYS cc_start: 0.8272 (mppt) cc_final: 0.7907 (tttt) REVERT: E 85 MET cc_start: 0.4529 (mpp) cc_final: 0.3846 (mpp) REVERT: E 258 MET cc_start: 0.3345 (tpp) cc_final: 0.3101 (tpp) REVERT: E 265 LYS cc_start: 0.3486 (pttt) cc_final: 0.2811 (tptp) REVERT: E 276 MET cc_start: -0.2316 (OUTLIER) cc_final: -0.3154 (tpt) REVERT: E 485 MET cc_start: 0.6548 (tpp) cc_final: 0.6267 (tmm) REVERT: E 631 GLU cc_start: 0.7742 (tp30) cc_final: 0.7274 (tp30) REVERT: E 635 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: E 731 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.4028 (p-80) outliers start: 72 outliers final: 55 residues processed: 334 average time/residue: 0.4687 time to fit residues: 268.0783 Evaluate side-chains 336 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 3.640 ------------------------------------------------------------------------------- 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 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 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE 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 422 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET 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 635 GLU 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 228 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 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 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 390 ILE 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 443 LEU 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 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 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 543 LEU Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 681 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 351 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 49 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 231 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** 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** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.209676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.148856 restraints weight = 62777.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.147705 restraints weight = 41872.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148566 restraints weight = 33157.430| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 31036 Z= 0.215 Angle : 0.746 12.534 42080 Z= 0.361 Chirality : 0.047 0.287 4786 Planarity : 0.005 0.081 5464 Dihedral : 6.687 124.664 4299 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.82 % Favored : 91.10 % Rotamer: Outliers : 2.22 % Allowed : 16.21 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3855 helix: 0.08 (0.13), residues: 1698 sheet: -2.36 (0.24), residues: 449 loop : -2.23 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 292 HIS 0.008 0.001 HIS C 726 PHE 0.018 0.001 PHE E 557 TYR 0.031 0.002 TYR D 225 ARG 0.011 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 1266) hydrogen bonds : angle 5.09935 ( 3672) covalent geometry : bond 0.00506 (31036) covalent geometry : angle 0.74627 (42080) ********************** 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 335 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 4.209 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 211 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8788 (pm20) REVERT: A 240 GLU cc_start: 0.4620 (tt0) cc_final: 0.3882 (tm-30) REVERT: A 247 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: A 331 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 505 TYR cc_start: 0.6942 (m-80) cc_final: 0.5850 (m-80) REVERT: A 544 GLU cc_start: 0.7896 (tt0) cc_final: 0.7689 (tt0) REVERT: B 230 MET cc_start: 0.3394 (mtt) cc_final: 0.3114 (mmp) REVERT: B 635 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: B 754 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7312 (mt) REVERT: B 768 TYR cc_start: 0.6942 (t80) cc_final: 0.6724 (t80) REVERT: C 625 LEU cc_start: 0.8301 (mt) cc_final: 0.8020 (mt) REVERT: D 217 MET cc_start: 0.5928 (tmm) cc_final: 0.5615 (ttp) REVERT: D 390 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7690 (mt) REVERT: D 426 LYS cc_start: 0.8325 (mppt) cc_final: 0.7952 (tttt) REVERT: D 516 MET cc_start: 0.8064 (mmm) cc_final: 0.7710 (mmm) REVERT: D 732 LYS cc_start: 0.7110 (mtmm) cc_final: 0.6603 (mtmm) REVERT: D 768 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: E 75 MET cc_start: 0.1713 (ptp) cc_final: 0.1394 (ptp) REVERT: E 85 MET cc_start: 0.4641 (mpp) cc_final: 0.3832 (mpp) REVERT: E 258 MET cc_start: 0.3315 (tpp) cc_final: 0.3000 (tpp) REVERT: E 265 LYS cc_start: 0.3617 (pttt) cc_final: 0.2919 (tptp) REVERT: E 276 MET cc_start: -0.2141 (OUTLIER) cc_final: -0.3103 (tpt) REVERT: E 485 MET cc_start: 0.6535 (tpp) cc_final: 0.6254 (tmm) REVERT: E 631 GLU cc_start: 0.7642 (tp30) cc_final: 0.7190 (tp30) REVERT: E 635 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: E 731 HIS cc_start: 0.4803 (OUTLIER) cc_final: 0.4285 (p-80) outliers start: 72 outliers final: 56 residues processed: 317 average time/residue: 0.4903 time to fit residues: 268.0275 Evaluate side-chains 328 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 4.169 ------------------------------------------------------------------------------- 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 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 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE 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 469 THR Chi-restraints excluded: chain B residue 485 MET 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 635 GLU 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 228 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 442 VAL 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 535 THR Chi-restraints excluded: chain C residue 617 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 273 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 390 ILE 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 443 LEU 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 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 20 THR 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 543 LEU Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 681 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 324 optimal weight: 30.0000 chunk 137 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 159 optimal weight: 0.0060 chunk 43 optimal weight: 10.0000 chunk 379 optimal weight: 0.0000 chunk 234 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 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 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.212803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158107 restraints weight = 61304.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155658 restraints weight = 37466.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155845 restraints weight = 27269.848| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31036 Z= 0.119 Angle : 0.669 12.406 42080 Z= 0.321 Chirality : 0.044 0.253 4786 Planarity : 0.005 0.080 5464 Dihedral : 6.379 123.449 4299 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 1.79 % Allowed : 16.76 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3855 helix: 0.34 (0.13), residues: 1693 sheet: -2.16 (0.24), residues: 444 loop : -2.08 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 292 HIS 0.005 0.001 HIS E 377 PHE 0.013 0.001 PHE E 557 TYR 0.015 0.001 TYR D 643 ARG 0.008 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 1266) hydrogen bonds : angle 4.78941 ( 3672) covalent geometry : bond 0.00268 (31036) covalent geometry : angle 0.66864 (42080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13591.32 seconds wall clock time: 243 minutes 54.32 seconds (14634.32 seconds total)