Starting phenix.real_space_refine on Mon Aug 25 20:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypj_34002/08_2025/7ypj_34002.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 5780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30478 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.63, per 1000 atoms: 0.25 Number of scatterers: 30478 At special positions: 0 Unit cell: (168.699, 169.76, 188.858, 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 5780 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 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: 151 helices and 36 sheets defined 48.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 4.288A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.548A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.592A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.764A 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 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.860A pdb=" N ASP A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.594A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.588A pdb=" N LYS A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 5.017A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.553A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.658A 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 386 through 391 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.561A 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 478 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.873A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.854A pdb=" N LYS A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.808A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.879A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.855A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.633A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.783A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.604A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.664A 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 137 removed outlier: 3.922A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.710A pdb=" N GLN B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 removed outlier: 3.899A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 186 through 237 Processing helix chain 'B' and resid 239 through 256 removed outlier: 3.530A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) 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 320 removed outlier: 3.732A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.786A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.974A pdb=" N GLN B 411 " --> pdb=" O HIS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 444 removed outlier: 4.565A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 443 " --> pdb=" O MET B 439 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.625A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.602A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.856A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.714A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 727 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 Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'C' and resid 29 through 39 removed outlier: 5.045A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 Processing helix chain 'C' and resid 140 through 143 Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 157 through 169 removed outlier: 4.172A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 184 through 238 removed outlier: 3.732A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 256 removed outlier: 3.561A pdb=" N LEU C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.535A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 removed outlier: 3.928A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 506 through 515 removed outlier: 3.527A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 515 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.617A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.674A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 717 through 727 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.938A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.809A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.738A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.749A pdb=" N GLY D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 184 through 238 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.953A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.634A pdb=" N THR D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.636A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 386 through 391 removed outlier: 4.165A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.572A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.770A pdb=" N ASP D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 4.064A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.624A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 534 Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.905A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 586 through 590 removed outlier: 4.221A pdb=" N THR D 590 " --> pdb=" O LYS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 646 Processing helix chain 'D' and resid 647 through 651 removed outlier: 3.625A pdb=" N ASP D 650 " --> pdb=" O HIS D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'D' and resid 679 through 692 removed outlier: 4.099A pdb=" N MET D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.508A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 726 " --> pdb=" O LEU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 3.748A pdb=" N LEU D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 4.602A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 770 Processing helix chain 'E' and resid 27 through 39 removed outlier: 4.310A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) 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 169 removed outlier: 3.508A pdb=" N ALA E 169 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.730A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 235 Processing helix chain 'E' and resid 237 through 245 Processing helix chain 'E' and resid 246 through 257 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 281 through 288 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.703A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.567A 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 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.530A pdb=" N LEU E 481 " --> pdb=" O PRO E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 514 removed outlier: 3.511A pdb=" N ALA E 502 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 523 through 534 Processing helix chain 'E' and resid 543 through 561 removed outlier: 4.182A pdb=" N LEU E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY E 561 " --> pdb=" O PHE E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.578A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 589 removed outlier: 4.175A pdb=" N LYS E 587 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 651 removed outlier: 4.158A pdb=" N THR E 642 " --> pdb=" O GLN E 638 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 659 removed outlier: 3.514A pdb=" N PHE E 657 " --> pdb=" O PRO E 654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 659 " --> pdb=" O ASP E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 693 removed outlier: 4.019A pdb=" N ALA E 684 " --> pdb=" O GLY E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 729 removed outlier: 3.578A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 738 No H-bonds generated for 'chain 'E' and resid 736 through 738' Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.379A pdb=" N GLU E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 770 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.731A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 71 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG A 89 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA A 69 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 91 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 67 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 93 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP A 65 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.731A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A 106 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR A 97 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 104 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.516A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.453A 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: 3.576A 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: 6.853A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 20 through 25 removed outlier: 7.836A pdb=" N LEU B 82 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 379 removed outlier: 6.356A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 598 through 603 removed outlier: 3.655A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 614 Processing sheet with id=AB2, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.616A pdb=" N VAL B 734 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.713A pdb=" N LEU C 5 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.725A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.725A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C 83 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.413A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP C 422 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 520 through 522 Processing sheet with id=AC1, first strand: chain 'C' and resid 592 through 593 Processing sheet with id=AC2, first strand: chain 'C' and resid 624 through 625 removed outlier: 5.923A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 705 through 707 removed outlier: 4.146A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.587A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE D 98 " --> pdb=" O ARG D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.535A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLN D 83 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA D 74 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 72 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.535A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 91 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AC8, first strand: chain 'D' and resid 377 through 378 removed outlier: 3.727A pdb=" N HIS D 377 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.779A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 617 through 618 removed outlier: 3.563A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL D 665 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 617 through 618 removed outlier: 3.563A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR D 608 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N MET D 702 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN D 598 " --> pdb=" O MET D 702 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.869A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP E 96 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 108 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL E 94 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 110 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 92 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.869A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP E 96 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 108 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL E 94 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 110 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 92 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 352 through 353 removed outlier: 7.682A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.832A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 468 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 421 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.049A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 732 through 733 1299 hydrogen bonds defined for protein. 3756 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: 7.04 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5772 1.32 - 1.45: 7324 1.45 - 1.58: 17713 1.58 - 1.70: 12 1.70 - 1.83: 210 Bond restraints: 31031 Sorted by residual: bond pdb=" C GLN E 229 " pdb=" O GLN E 229 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.78e+01 bond pdb=" CB MET D 427 " pdb=" CG MET D 427 " ideal model delta sigma weight residual 1.520 1.415 0.105 3.00e-02 1.11e+03 1.24e+01 bond pdb=" N ILE D 681 " pdb=" CA ILE D 681 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.26e-02 6.30e+03 9.09e+00 bond pdb=" N VAL A 54 " pdb=" CA VAL A 54 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.95e+00 bond pdb=" CA LEU C 421 " pdb=" CB LEU C 421 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.53e-02 4.27e+03 8.91e+00 ... (remaining 31026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 41099 3.58 - 7.16: 878 7.16 - 10.73: 83 10.73 - 14.31: 11 14.31 - 17.89: 4 Bond angle restraints: 42075 Sorted by residual: angle pdb=" CA PRO A 714 " pdb=" N PRO A 714 " pdb=" CD PRO A 714 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 angle pdb=" N GLY E 358 " pdb=" CA GLY E 358 " pdb=" C GLY E 358 " ideal model delta sigma weight residual 113.99 121.13 -7.14 1.28e+00 6.10e-01 3.11e+01 angle pdb=" N GLN E 229 " pdb=" CA GLN E 229 " pdb=" C GLN E 229 " ideal model delta sigma weight residual 110.97 104.97 6.00 1.09e+00 8.42e-01 3.03e+01 angle pdb=" C ALA A 400 " pdb=" N MET A 401 " pdb=" CA MET A 401 " ideal model delta sigma weight residual 122.90 111.57 11.33 2.07e+00 2.33e-01 2.99e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 107.70 101.40 6.30 1.22e+00 6.72e-01 2.66e+01 ... (remaining 42070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.63: 18706 30.63 - 61.25: 393 61.25 - 91.88: 42 91.88 - 122.50: 0 122.50 - 153.13: 3 Dihedral angle restraints: 19144 sinusoidal: 7989 harmonic: 11155 Sorted by residual: dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 146.88 153.13 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 164.64 135.35 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O2A ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PA ADP C 801 " pdb=" PB ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 172.24 127.76 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 19141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4352 0.110 - 0.221: 404 0.221 - 0.331: 28 0.331 - 0.442: 1 0.442 - 0.552: 1 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CG LEU C 629 " pdb=" CB LEU C 629 " pdb=" CD1 LEU C 629 " pdb=" CD2 LEU C 629 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CG LEU A 751 " pdb=" CB LEU A 751 " pdb=" CD1 LEU A 751 " pdb=" CD2 LEU A 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CG LEU C 722 " pdb=" CB LEU C 722 " pdb=" CD1 LEU C 722 " pdb=" CD2 LEU C 722 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 4783 not shown) Planarity restraints: 5464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 713 " 0.069 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 714 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 714 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 714 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 171 " -0.023 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP E 171 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP E 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 171 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 171 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP E 171 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 171 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 171 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 171 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 228 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLU E 228 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 228 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 229 " -0.019 2.00e-02 2.50e+03 ... (remaining 5461 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1993 2.71 - 3.26: 32599 3.26 - 3.81: 54300 3.81 - 4.35: 67257 4.35 - 4.90: 104778 Nonbonded interactions: 260927 Sorted by model distance: nonbonded pdb=" O ALA D 639 " pdb=" OG1 THR D 642 " model vdw 2.167 3.040 nonbonded pdb=" O LEU D 528 " pdb=" OG SER D 532 " model vdw 2.177 3.040 nonbonded pdb=" O LEU D 364 " pdb=" OG SER D 367 " model vdw 2.185 3.040 nonbonded pdb=" O MET A 160 " pdb=" OG1 THR A 164 " model vdw 2.194 3.040 nonbonded pdb=" O ALA A 678 " pdb=" OG1 THR A 703 " model vdw 2.201 3.040 ... (remaining 260922 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: 3.170 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: 0.060 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.570 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 31031 Z= 0.398 Angle : 1.265 17.891 42075 Z= 0.708 Chirality : 0.066 0.552 4786 Planarity : 0.008 0.098 5464 Dihedral : 13.225 153.127 11964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 0.12 % Allowed : 1.08 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.12), residues: 3855 helix: -1.16 (0.12), residues: 1615 sheet: -2.43 (0.25), residues: 360 loop : -2.40 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 378 TYR 0.036 0.003 TYR C 460 PHE 0.050 0.003 PHE E 467 TRP 0.053 0.005 TRP E 171 HIS 0.016 0.003 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00786 (31031) covalent geometry : angle 1.26486 (42075) hydrogen bonds : bond 0.19258 ( 1287) hydrogen bonds : angle 8.11545 ( 3756) *********************** 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 217 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8354 (mmp) cc_final: 0.7993 (mmm) REVERT: A 698 MET cc_start: 0.4634 (mtt) cc_final: 0.3781 (mtt) REVERT: B 230 MET cc_start: 0.8760 (ttp) cc_final: 0.8456 (ppp) REVERT: B 351 LEU cc_start: 0.9292 (tp) cc_final: 0.9067 (tp) REVERT: B 379 ILE cc_start: 0.9565 (tp) cc_final: 0.9250 (tt) REVERT: B 409 MET cc_start: 0.9057 (tpt) cc_final: 0.8479 (tpp) REVERT: C 422 ASP cc_start: 0.8557 (t70) cc_final: 0.8332 (t0) REVERT: C 476 THR cc_start: 0.8976 (t) cc_final: 0.8737 (p) REVERT: C 483 ASP cc_start: 0.8804 (p0) cc_final: 0.8536 (p0) REVERT: C 711 LYS cc_start: 0.8909 (mptt) cc_final: 0.8680 (mmmt) REVERT: D 230 MET cc_start: 0.8295 (tmm) cc_final: 0.7813 (tmm) REVERT: D 317 GLU cc_start: 0.8345 (pp20) cc_final: 0.8083 (pp20) REVERT: D 401 MET cc_start: 0.9120 (ttp) cc_final: 0.8899 (pmm) REVERT: D 426 LYS cc_start: 0.9311 (mtmt) cc_final: 0.9108 (mmtm) REVERT: D 713 MET cc_start: 0.8723 (tpt) cc_final: 0.8471 (tpp) REVERT: E 235 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9384 (tptp) REVERT: E 255 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: E 657 PHE cc_start: 0.9066 (t80) cc_final: 0.8640 (t80) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.1729 time to fit residues: 61.1048 Evaluate side-chains 174 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN B 83 GLN B 220 ASN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.091073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.068595 restraints weight = 136028.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.068404 restraints weight = 151621.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.068291 restraints weight = 151860.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.068277 restraints weight = 152557.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.068274 restraints weight = 152312.024| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31031 Z= 0.141 Angle : 0.736 11.718 42075 Z= 0.367 Chirality : 0.045 0.263 4786 Planarity : 0.006 0.061 5464 Dihedral : 7.652 136.904 4304 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.52 % Allowed : 6.79 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.13), residues: 3855 helix: -0.50 (0.12), residues: 1655 sheet: -2.32 (0.26), residues: 354 loop : -2.24 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 395 TYR 0.020 0.002 TYR D 643 PHE 0.010 0.001 PHE E 467 TRP 0.022 0.002 TRP E 171 HIS 0.007 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00294 (31031) covalent geometry : angle 0.73594 (42075) hydrogen bonds : bond 0.04788 ( 1287) hydrogen bonds : angle 5.96729 ( 3756) *********************** 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 205 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8088 (mmp) cc_final: 0.7742 (mmm) REVERT: C 258 MET cc_start: 0.3780 (mtt) cc_final: 0.3413 (mtt) REVERT: C 409 MET cc_start: 0.8744 (tpp) cc_final: 0.8529 (tpp) REVERT: C 422 ASP cc_start: 0.8411 (t70) cc_final: 0.8177 (t0) REVERT: C 476 THR cc_start: 0.8638 (t) cc_final: 0.8413 (p) REVERT: C 663 LEU cc_start: 0.9343 (tp) cc_final: 0.9136 (mp) REVERT: D 317 GLU cc_start: 0.8039 (pp20) cc_final: 0.7787 (pp20) REVERT: D 516 MET cc_start: 0.7535 (ttm) cc_final: 0.6298 (mmm) REVERT: E 85 MET cc_start: 0.6682 (mpp) cc_final: 0.6307 (mpp) REVERT: E 516 MET cc_start: 0.1535 (mtm) cc_final: 0.1273 (mtt) REVERT: E 657 PHE cc_start: 0.9065 (t80) cc_final: 0.8652 (t80) outliers start: 17 outliers final: 7 residues processed: 198 average time/residue: 0.1518 time to fit residues: 49.9128 Evaluate side-chains 180 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 255 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 chunk 382 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 304 optimal weight: 0.6980 chunk 359 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 290 optimal weight: 0.0010 chunk 263 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.086563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.063162 restraints weight = 145957.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.062930 restraints weight = 168839.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.062854 restraints weight = 170259.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.062854 restraints weight = 164545.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.062854 restraints weight = 164545.557| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31031 Z= 0.216 Angle : 0.755 12.363 42075 Z= 0.379 Chirality : 0.045 0.299 4786 Planarity : 0.006 0.067 5464 Dihedral : 7.500 132.938 4302 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.27 % Allowed : 9.20 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.13), residues: 3855 helix: -0.19 (0.13), residues: 1650 sheet: -2.35 (0.26), residues: 367 loop : -2.17 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 212 TYR 0.027 0.002 TYR D 643 PHE 0.014 0.001 PHE E 467 TRP 0.022 0.002 TRP E 298 HIS 0.007 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00450 (31031) covalent geometry : angle 0.75499 (42075) hydrogen bonds : bond 0.04704 ( 1287) hydrogen bonds : angle 5.81825 ( 3756) *********************** 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 216 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.4733 (pm20) REVERT: A 85 MET cc_start: 0.8102 (mmp) cc_final: 0.7755 (mmm) REVERT: A 401 MET cc_start: 0.9095 (ppp) cc_final: 0.8810 (ppp) REVERT: A 427 MET cc_start: 0.4959 (ttt) cc_final: 0.4737 (tpt) REVERT: A 698 MET cc_start: 0.3561 (mtt) cc_final: 0.2379 (mtt) REVERT: B 230 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7889 (ppp) REVERT: B 633 MET cc_start: 0.8661 (mmm) cc_final: 0.8416 (mmm) REVERT: B 663 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8461 (mm) REVERT: C 230 MET cc_start: 0.9218 (ppp) cc_final: 0.8982 (ppp) REVERT: C 258 MET cc_start: 0.3009 (mtt) cc_final: 0.2703 (mtt) REVERT: C 422 ASP cc_start: 0.8115 (t70) cc_final: 0.7908 (t0) REVERT: C 439 MET cc_start: 0.9659 (mmm) cc_final: 0.9346 (mmm) REVERT: C 476 THR cc_start: 0.8707 (t) cc_final: 0.8443 (p) REVERT: C 483 ASP cc_start: 0.8363 (p0) cc_final: 0.8154 (p0) REVERT: C 501 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8186 (tt) REVERT: D 160 MET cc_start: 0.1384 (OUTLIER) cc_final: 0.0441 (ppp) REVERT: D 317 GLU cc_start: 0.8170 (pp20) cc_final: 0.7853 (pp20) REVERT: D 499 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: D 713 MET cc_start: 0.8151 (tpp) cc_final: 0.7622 (tpp) REVERT: D 727 GLN cc_start: 0.5143 (OUTLIER) cc_final: 0.4794 (mm-40) REVERT: E 75 MET cc_start: 0.4432 (pmm) cc_final: 0.3990 (pmm) REVERT: E 423 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: E 657 PHE cc_start: 0.9142 (t80) cc_final: 0.8751 (t80) outliers start: 41 outliers final: 14 residues processed: 207 average time/residue: 0.1649 time to fit residues: 57.0556 Evaluate side-chains 189 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 713 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 210 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 363 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS D 411 GLN D 593 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.099578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072226 restraints weight = 281406.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.071700 restraints weight = 248490.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071001 restraints weight = 219134.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.070999 restraints weight = 165696.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.071150 restraints weight = 152891.447| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31031 Z= 0.186 Angle : 0.726 12.569 42075 Z= 0.361 Chirality : 0.045 0.260 4786 Planarity : 0.005 0.058 5464 Dihedral : 7.352 133.283 4302 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.57 % Allowed : 11.23 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.13), residues: 3855 helix: -0.05 (0.13), residues: 1659 sheet: -2.25 (0.26), residues: 366 loop : -2.10 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 345 TYR 0.025 0.002 TYR D 643 PHE 0.013 0.001 PHE D 467 TRP 0.023 0.002 TRP E 298 HIS 0.007 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00386 (31031) covalent geometry : angle 0.72646 (42075) hydrogen bonds : bond 0.04270 ( 1287) hydrogen bonds : angle 5.59691 ( 3756) *********************** 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 228 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: A 401 MET cc_start: 0.9105 (ppp) cc_final: 0.8836 (ppp) REVERT: A 427 MET cc_start: 0.4427 (ttt) cc_final: 0.3997 (tpt) REVERT: A 496 MET cc_start: 0.8650 (mmp) cc_final: 0.8308 (mmp) REVERT: B 427 MET cc_start: 0.6728 (mmp) cc_final: 0.5976 (mmp) REVERT: B 613 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: B 663 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 258 MET cc_start: 0.3147 (mtt) cc_final: 0.2876 (mtt) REVERT: C 439 MET cc_start: 0.9565 (mmm) cc_final: 0.9159 (mmm) REVERT: D 160 MET cc_start: 0.1365 (mmp) cc_final: 0.0638 (ppp) REVERT: D 317 GLU cc_start: 0.8196 (pp20) cc_final: 0.7926 (pp20) REVERT: D 499 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7743 (mm-40) REVERT: D 531 ILE cc_start: 0.8569 (mp) cc_final: 0.7943 (mp) REVERT: D 713 MET cc_start: 0.8560 (tpp) cc_final: 0.8085 (tpp) REVERT: E 372 MET cc_start: 0.5391 (tpp) cc_final: 0.5109 (tpp) REVERT: E 423 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: E 657 PHE cc_start: 0.9068 (t80) cc_final: 0.8504 (t80) outliers start: 51 outliers final: 25 residues processed: 219 average time/residue: 0.1612 time to fit residues: 58.6740 Evaluate side-chains 197 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 259 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 334 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 57 optimal weight: 0.0770 chunk 118 optimal weight: 8.9990 chunk 266 optimal weight: 0.0770 chunk 342 optimal weight: 0.2980 overall best weight: 2.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** D 319 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 = 0.4376 r_free = 0.4376 target = 0.100021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.072167 restraints weight = 281651.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.072092 restraints weight = 240935.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.071642 restraints weight = 204926.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.072059 restraints weight = 195602.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.071182 restraints weight = 143566.160| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31031 Z= 0.149 Angle : 0.692 11.219 42075 Z= 0.341 Chirality : 0.044 0.243 4786 Planarity : 0.005 0.053 5464 Dihedral : 7.174 134.160 4302 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.60 % Allowed : 12.35 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.14), residues: 3855 helix: 0.08 (0.13), residues: 1668 sheet: -2.14 (0.26), residues: 359 loop : -2.01 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 479 TYR 0.019 0.001 TYR D 643 PHE 0.009 0.001 PHE D 467 TRP 0.019 0.002 TRP E 298 HIS 0.005 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00315 (31031) covalent geometry : angle 0.69192 (42075) hydrogen bonds : bond 0.03958 ( 1287) hydrogen bonds : angle 5.39616 ( 3756) *********************** 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 226 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.8273 (tpt90) cc_final: 0.7905 (tpt90) REVERT: A 401 MET cc_start: 0.9016 (ppp) cc_final: 0.8736 (ppp) REVERT: A 427 MET cc_start: 0.4167 (ttt) cc_final: 0.3885 (ttt) REVERT: A 496 MET cc_start: 0.8721 (mmp) cc_final: 0.8324 (mmp) REVERT: B 427 MET cc_start: 0.6042 (mmp) cc_final: 0.5550 (mmp) REVERT: B 633 MET cc_start: 0.8488 (mmp) cc_final: 0.7998 (mmm) REVERT: C 258 MET cc_start: 0.2792 (mtt) cc_final: 0.2556 (mtt) REVERT: C 439 MET cc_start: 0.9559 (mmm) cc_final: 0.9152 (mmm) REVERT: C 483 ASP cc_start: 0.8397 (p0) cc_final: 0.8017 (p0) REVERT: D 160 MET cc_start: 0.1205 (mmp) cc_final: 0.0445 (ppp) REVERT: D 317 GLU cc_start: 0.8208 (pp20) cc_final: 0.7925 (pp20) REVERT: D 499 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7777 (mm-40) REVERT: D 531 ILE cc_start: 0.8312 (mp) cc_final: 0.7766 (mp) REVERT: D 713 MET cc_start: 0.8587 (tpp) cc_final: 0.8216 (tpp) REVERT: E 423 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: E 657 PHE cc_start: 0.8905 (t80) cc_final: 0.8488 (t80) outliers start: 52 outliers final: 22 residues processed: 221 average time/residue: 0.1863 time to fit residues: 68.9853 Evaluate side-chains 194 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 121 optimal weight: 9.9990 chunk 297 optimal weight: 0.0000 chunk 315 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 152 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 598 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN E 472 ASN E 666 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.101281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.073670 restraints weight = 278780.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.071420 restraints weight = 229769.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.072198 restraints weight = 171152.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.072060 restraints weight = 137737.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.072060 restraints weight = 120473.118| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31031 Z= 0.119 Angle : 0.676 11.428 42075 Z= 0.327 Chirality : 0.043 0.189 4786 Planarity : 0.005 0.051 5464 Dihedral : 6.828 133.938 4299 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.30 % Allowed : 13.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.14), residues: 3855 helix: 0.26 (0.13), residues: 1673 sheet: -2.05 (0.26), residues: 349 loop : -1.89 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 385 TYR 0.015 0.001 TYR E 224 PHE 0.008 0.001 PHE E 466 TRP 0.016 0.001 TRP E 298 HIS 0.005 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00256 (31031) covalent geometry : angle 0.67644 (42075) hydrogen bonds : bond 0.03620 ( 1287) hydrogen bonds : angle 5.16240 ( 3756) *********************** 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 226 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 MET cc_start: 0.8923 (ppp) cc_final: 0.8714 (ppp) REVERT: A 427 MET cc_start: 0.4742 (ttt) cc_final: 0.4332 (ttt) REVERT: A 496 MET cc_start: 0.8704 (mmp) cc_final: 0.8313 (mmp) REVERT: A 698 MET cc_start: 0.3148 (mtt) cc_final: 0.1466 (mtt) REVERT: B 427 MET cc_start: 0.6247 (mmp) cc_final: 0.5851 (mmp) REVERT: B 472 ASN cc_start: 0.8644 (t0) cc_final: 0.8262 (p0) REVERT: B 633 MET cc_start: 0.8694 (mmp) cc_final: 0.8250 (mmm) REVERT: C 276 MET cc_start: 0.8327 (tmm) cc_final: 0.8021 (tmm) REVERT: C 439 MET cc_start: 0.9463 (mmm) cc_final: 0.8919 (mmm) REVERT: C 443 LEU cc_start: 0.9548 (mt) cc_final: 0.9271 (mt) REVERT: D 160 MET cc_start: 0.1310 (OUTLIER) cc_final: 0.0588 (ppp) REVERT: D 230 MET cc_start: 0.8257 (tmm) cc_final: 0.7919 (tmm) REVERT: D 317 GLU cc_start: 0.8186 (pp20) cc_final: 0.7877 (pp20) REVERT: D 499 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7885 (mm-40) REVERT: D 531 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7894 (mp) REVERT: D 713 MET cc_start: 0.8559 (tpp) cc_final: 0.8288 (tpp) REVERT: E 276 MET cc_start: 0.6087 (mmm) cc_final: 0.5576 (mmm) REVERT: E 372 MET cc_start: 0.5108 (mmp) cc_final: 0.3500 (tpp) REVERT: E 657 PHE cc_start: 0.8935 (t80) cc_final: 0.8501 (t80) outliers start: 42 outliers final: 25 residues processed: 220 average time/residue: 0.1865 time to fit residues: 69.1343 Evaluate side-chains 198 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 28 optimal weight: 2.9990 chunk 251 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 321 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** 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 = 0.4306 r_free = 0.4306 target = 0.082383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.058542 restraints weight = 148964.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.058308 restraints weight = 156021.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.058303 restraints weight = 159360.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.058309 restraints weight = 154740.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.058309 restraints weight = 154172.118| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 31031 Z= 0.293 Angle : 0.854 18.051 42075 Z= 0.429 Chirality : 0.047 0.248 4786 Planarity : 0.006 0.059 5464 Dihedral : 7.293 132.516 4299 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.38 % Allowed : 14.14 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.13), residues: 3855 helix: -0.16 (0.12), residues: 1682 sheet: -2.03 (0.26), residues: 365 loop : -2.00 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 345 TYR 0.034 0.002 TYR D 643 PHE 0.017 0.002 PHE C 466 TRP 0.022 0.002 TRP E 298 HIS 0.010 0.002 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00606 (31031) covalent geometry : angle 0.85409 (42075) hydrogen bonds : bond 0.04635 ( 1287) hydrogen bonds : angle 5.66471 ( 3756) *********************** 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 246 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 169 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.5161 (ttt) cc_final: 0.4948 (ttt) REVERT: A 496 MET cc_start: 0.8333 (mmp) cc_final: 0.7994 (mmp) REVERT: A 625 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9221 (tp) REVERT: A 698 MET cc_start: 0.3452 (mtt) cc_final: 0.2236 (mtt) REVERT: B 567 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6956 (mtt-85) REVERT: B 633 MET cc_start: 0.9043 (mmp) cc_final: 0.8445 (mmm) REVERT: C 439 MET cc_start: 0.9760 (mmm) cc_final: 0.9474 (mmm) REVERT: D 160 MET cc_start: 0.1591 (OUTLIER) cc_final: 0.0629 (ppp) REVERT: D 317 GLU cc_start: 0.8224 (pp20) cc_final: 0.7937 (pp20) REVERT: D 499 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: D 531 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 713 MET cc_start: 0.8812 (tpp) cc_final: 0.8472 (tpp) REVERT: E 276 MET cc_start: 0.5629 (mmm) cc_final: 0.5339 (mmm) REVERT: E 409 MET cc_start: 0.8658 (tpp) cc_final: 0.8244 (tpp) REVERT: E 423 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: E 427 MET cc_start: 0.8612 (mmm) cc_final: 0.8250 (mmm) REVERT: E 657 PHE cc_start: 0.9062 (t80) cc_final: 0.8654 (t80) outliers start: 77 outliers final: 46 residues processed: 231 average time/residue: 0.1680 time to fit residues: 65.2152 Evaluate side-chains 214 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 216 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 309 optimal weight: 40.0000 chunk 56 optimal weight: 9.9990 chunk 90 optimal weight: 50.0000 chunk 178 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** E 310 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 = 0.4363 r_free = 0.4363 target = 0.099246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071417 restraints weight = 281435.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.070194 restraints weight = 241315.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.070185 restraints weight = 189355.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.069762 restraints weight = 136848.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.069745 restraints weight = 146056.197| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31031 Z= 0.149 Angle : 0.739 13.801 42075 Z= 0.360 Chirality : 0.045 0.244 4786 Planarity : 0.005 0.050 5464 Dihedral : 7.063 133.306 4299 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.67 % Allowed : 15.46 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3855 helix: 0.16 (0.13), residues: 1666 sheet: -1.98 (0.26), residues: 365 loop : -1.91 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 479 TYR 0.019 0.002 TYR D 643 PHE 0.008 0.001 PHE D 376 TRP 0.014 0.002 TRP E 298 HIS 0.006 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00321 (31031) covalent geometry : angle 0.73945 (42075) hydrogen bonds : bond 0.03872 ( 1287) hydrogen bonds : angle 5.31216 ( 3756) *********************** 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 226 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.872 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 427 MET cc_start: 0.4610 (ttt) cc_final: 0.4294 (ttt) REVERT: A 496 MET cc_start: 0.8705 (mmp) cc_final: 0.8329 (mmp) REVERT: A 625 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9124 (tp) REVERT: A 698 MET cc_start: 0.3745 (mtt) cc_final: 0.2687 (mtt) REVERT: B 472 ASN cc_start: 0.8628 (t0) cc_final: 0.8044 (t0) REVERT: B 485 MET cc_start: 0.8202 (mpp) cc_final: 0.7588 (mpp) REVERT: B 633 MET cc_start: 0.8809 (mmp) cc_final: 0.8269 (mmm) REVERT: C 276 MET cc_start: 0.8338 (tmm) cc_final: 0.7990 (tmm) REVERT: C 423 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: C 439 MET cc_start: 0.9581 (mmm) cc_final: 0.9059 (mmm) REVERT: C 443 LEU cc_start: 0.9566 (mt) cc_final: 0.9296 (mt) REVERT: C 633 MET cc_start: 0.8531 (ptt) cc_final: 0.8242 (pmm) REVERT: D 160 MET cc_start: 0.1356 (OUTLIER) cc_final: 0.0623 (ppp) REVERT: D 276 MET cc_start: 0.3354 (ppp) cc_final: 0.3121 (ppp) REVERT: D 317 GLU cc_start: 0.8158 (pp20) cc_final: 0.7817 (pp20) REVERT: D 499 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7828 (mm-40) REVERT: D 531 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.7880 (mp) REVERT: D 713 MET cc_start: 0.8697 (tpp) cc_final: 0.8368 (tpp) REVERT: E 276 MET cc_start: 0.6033 (mmm) cc_final: 0.5619 (mmm) REVERT: E 372 MET cc_start: 0.5651 (mmp) cc_final: 0.4092 (tpp) REVERT: E 657 PHE cc_start: 0.8974 (t80) cc_final: 0.8546 (t80) outliers start: 54 outliers final: 33 residues processed: 218 average time/residue: 0.1587 time to fit residues: 58.2083 Evaluate side-chains 202 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 319 optimal weight: 50.0000 chunk 237 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 92 optimal weight: 50.0000 chunk 55 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.083830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.059508 restraints weight = 145776.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.059484 restraints weight = 149449.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.059466 restraints weight = 148304.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.059466 restraints weight = 148157.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.059466 restraints weight = 148157.276| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31031 Z= 0.212 Angle : 0.798 16.872 42075 Z= 0.392 Chirality : 0.046 0.243 4786 Planarity : 0.005 0.055 5464 Dihedral : 7.155 131.935 4299 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.21 % Favored : 90.77 % Rotamer: Outliers : 1.64 % Allowed : 15.40 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3855 helix: 0.00 (0.13), residues: 1684 sheet: -2.08 (0.27), residues: 348 loop : -1.94 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 479 TYR 0.027 0.002 TYR D 643 PHE 0.012 0.001 PHE C 466 TRP 0.026 0.002 TRP E 298 HIS 0.008 0.002 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00446 (31031) covalent geometry : angle 0.79822 (42075) hydrogen bonds : bond 0.04165 ( 1287) hydrogen bonds : angle 5.43285 ( 3756) *********************** 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 224 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 1.151 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 160 MET cc_start: 0.7582 (mmm) cc_final: 0.7295 (mmm) REVERT: A 496 MET cc_start: 0.8314 (mmp) cc_final: 0.7971 (mmp) REVERT: A 625 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9267 (tp) REVERT: A 698 MET cc_start: 0.3582 (mtt) cc_final: 0.2375 (mtt) REVERT: B 472 ASN cc_start: 0.9513 (t0) cc_final: 0.9302 (t0) REVERT: B 485 MET cc_start: 0.8663 (mpp) cc_final: 0.8041 (mpp) REVERT: B 567 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6921 (mtt-85) REVERT: B 633 MET cc_start: 0.9056 (mmp) cc_final: 0.8416 (mmm) REVERT: C 276 MET cc_start: 0.8603 (tmm) cc_final: 0.8293 (tmm) REVERT: C 439 MET cc_start: 0.9747 (mmm) cc_final: 0.9466 (mmm) REVERT: D 160 MET cc_start: 0.1647 (OUTLIER) cc_final: 0.0666 (ppp) REVERT: D 317 GLU cc_start: 0.8282 (pp20) cc_final: 0.7957 (pp20) REVERT: D 499 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7639 (mm-40) REVERT: D 531 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7840 (mp) REVERT: D 698 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4429 (tmm) REVERT: D 713 MET cc_start: 0.8702 (tpp) cc_final: 0.8452 (tpp) REVERT: E 276 MET cc_start: 0.5827 (mmm) cc_final: 0.5536 (mmm) REVERT: E 409 MET cc_start: 0.8810 (tpp) cc_final: 0.8402 (tpp) REVERT: E 427 MET cc_start: 0.8423 (mmm) cc_final: 0.8111 (mmm) REVERT: E 657 PHE cc_start: 0.9077 (t80) cc_final: 0.8674 (t80) outliers start: 53 outliers final: 40 residues processed: 213 average time/residue: 0.1626 time to fit residues: 59.1483 Evaluate side-chains 209 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 198 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 118 optimal weight: 0.4980 chunk 330 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.085323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.060881 restraints weight = 139543.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.060881 restraints weight = 146613.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.060880 restraints weight = 146633.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.060880 restraints weight = 146632.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.060880 restraints weight = 146632.979| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31031 Z= 0.168 Angle : 0.775 16.309 42075 Z= 0.378 Chirality : 0.045 0.241 4786 Planarity : 0.005 0.053 5464 Dihedral : 7.067 131.905 4299 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.54 % Allowed : 15.96 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.14), residues: 3855 helix: 0.08 (0.13), residues: 1684 sheet: -2.24 (0.25), residues: 385 loop : -1.87 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 479 TYR 0.019 0.002 TYR D 643 PHE 0.010 0.001 PHE E 466 TRP 0.019 0.002 TRP E 298 HIS 0.007 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00361 (31031) covalent geometry : angle 0.77491 (42075) hydrogen bonds : bond 0.03896 ( 1287) hydrogen bonds : angle 5.30559 ( 3756) ********************** 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 220 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 1.053 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 38 MET cc_start: 0.7258 (ptp) cc_final: 0.6955 (pmm) REVERT: A 160 MET cc_start: 0.7540 (mmm) cc_final: 0.7247 (mmm) REVERT: A 496 MET cc_start: 0.8241 (mmp) cc_final: 0.7892 (mmp) REVERT: A 625 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9320 (tp) REVERT: A 698 MET cc_start: 0.3363 (mtt) cc_final: 0.2266 (mtt) REVERT: B 485 MET cc_start: 0.8585 (mpp) cc_final: 0.8023 (mpp) REVERT: B 567 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: B 633 MET cc_start: 0.8960 (mmp) cc_final: 0.8375 (mmm) REVERT: C 276 MET cc_start: 0.8682 (tmm) cc_final: 0.8454 (tmm) REVERT: C 439 MET cc_start: 0.9747 (mmm) cc_final: 0.9285 (mmm) REVERT: C 443 LEU cc_start: 0.9525 (mt) cc_final: 0.9266 (mt) REVERT: C 633 MET cc_start: 0.9016 (ptt) cc_final: 0.8691 (pmm) REVERT: D 160 MET cc_start: 0.1528 (OUTLIER) cc_final: 0.0501 (ppp) REVERT: D 317 GLU cc_start: 0.8274 (pp20) cc_final: 0.7978 (pp20) REVERT: D 401 MET cc_start: 0.8532 (ppp) cc_final: 0.8068 (ppp) REVERT: D 499 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (mm-40) REVERT: D 531 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7945 (mp) REVERT: D 698 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4810 (tmm) REVERT: D 713 MET cc_start: 0.8675 (tpp) cc_final: 0.8427 (tpp) REVERT: E 276 MET cc_start: 0.5730 (mmm) cc_final: 0.5455 (mmm) REVERT: E 427 MET cc_start: 0.8551 (mmm) cc_final: 0.8211 (mmm) REVERT: E 509 LYS cc_start: 0.9047 (pttm) cc_final: 0.8808 (pptt) REVERT: E 657 PHE cc_start: 0.9108 (t80) cc_final: 0.8679 (t80) outliers start: 50 outliers final: 41 residues processed: 208 average time/residue: 0.1580 time to fit residues: 55.1239 Evaluate side-chains 215 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 226 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 365 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.098094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.070023 restraints weight = 283728.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.068611 restraints weight = 232329.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.069131 restraints weight = 190044.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.068527 restraints weight = 142979.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.068602 restraints weight = 144194.331| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31031 Z= 0.174 Angle : 0.779 17.177 42075 Z= 0.379 Chirality : 0.045 0.223 4786 Planarity : 0.005 0.063 5464 Dihedral : 7.014 131.290 4299 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.54 % Allowed : 16.14 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3855 helix: 0.11 (0.13), residues: 1690 sheet: -2.23 (0.26), residues: 387 loop : -1.86 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 479 TYR 0.021 0.002 TYR D 643 PHE 0.011 0.001 PHE E 466 TRP 0.023 0.002 TRP E 298 HIS 0.008 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00371 (31031) covalent geometry : angle 0.77877 (42075) hydrogen bonds : bond 0.03853 ( 1287) hydrogen bonds : angle 5.27120 ( 3756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7809.42 seconds wall clock time: 134 minutes 43.05 seconds (8083.05 seconds total)