Starting phenix.real_space_refine on Tue Aug 26 11:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yux_34114/08_2025/7yux_34114.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yux_34114/08_2025/7yux_34114.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/7yux_34114/08_2025/7yux_34114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yux_34114/08_2025/7yux_34114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yux_34114/08_2025/7yux_34114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yux_34114/08_2025/7yux_34114.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= 0.002 sd= 0.037 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 10 5.49 5 S 126 5.16 5 C 23078 2.51 5 N 6427 2.21 5 O 6944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s 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: 36585 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" 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: "E" 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} Chain: "B" 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: 7.24, per 1000 atoms: 0.20 Number of scatterers: 36585 At special positions: 0 Unit cell: (174.66, 155.8, 179.58, 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 126 16.00 P 10 15.00 O 6944 8.00 N 6427 7.00 C 23078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 42 sheets defined 47.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 removed outlier: 4.197A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.646A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.928A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.799A pdb=" N VAL A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 172 through 182 removed outlier: 4.180A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 237 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.733A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.609A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.649A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.642A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.713A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.682A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.218A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.798A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.661A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.688A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.967A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.159A pdb=" N GLU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.745A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.675A pdb=" N VAL C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 138 removed outlier: 3.640A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.820A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 234 removed outlier: 3.686A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.895A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.836A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.945A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 434 through 442 removed outlier: 4.457A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.665A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.570A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 506 through 515 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.933A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 630 through 646 removed outlier: 3.743A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.930A pdb=" N ALA C 728 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.707A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.552A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 4.286A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 139 removed outlier: 3.719A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.795A pdb=" N LEU E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 150 " --> pdb=" O TYR E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 150' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.738A pdb=" N LEU E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 234 Processing helix chain 'E' and resid 239 through 256 removed outlier: 4.291A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 308 through 319 removed outlier: 3.708A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 337 removed outlier: 4.336A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.177A pdb=" N ASP E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.808A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 648 through 652 removed outlier: 4.277A pdb=" N GLY E 652 " --> pdb=" O GLN E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.749A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 761 through 767 removed outlier: 4.164A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 removed outlier: 4.201A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.633A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 184 through 234 Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.705A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.586A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.026A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.633A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 386 through 391 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.582A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 473 through 477 Processing helix chain 'D' and resid 494 through 506 removed outlier: 3.599A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 515 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.657A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 586 through 590 removed outlier: 3.517A pdb=" N GLU D 589 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.560A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 742 through 746 removed outlier: 3.773A pdb=" N LEU D 746 " --> pdb=" O LEU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 761 through 769 removed outlier: 3.835A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.562A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 139 removed outlier: 3.565A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 removed outlier: 3.934A pdb=" N LEU F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 Processing helix chain 'F' and resid 173 through 182 Processing helix chain 'F' and resid 184 through 235 removed outlier: 3.512A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS F 235 " --> pdb=" O LYS F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.480A pdb=" N ALA F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 272 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 308 through 317 Processing helix chain 'F' and resid 324 through 338 removed outlier: 4.038A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 Processing helix chain 'F' and resid 403 through 412 Processing helix chain 'F' and resid 434 through 444 removed outlier: 4.456A pdb=" N ALA F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 483 removed outlier: 3.880A pdb=" N ASP F 483 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 515 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 541 through 560 Processing helix chain 'F' and resid 573 through 578 removed outlier: 4.048A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 647 Processing helix chain 'F' and resid 648 through 651 removed outlier: 3.603A pdb=" N TYR F 651 " --> pdb=" O THR F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 679 through 693 removed outlier: 3.527A pdb=" N MET F 683 " --> pdb=" O ALA F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.723A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 745 removed outlier: 4.407A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 761 through 767 removed outlier: 3.618A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 118 through 137 Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.236A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.827A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.906A pdb=" N GLN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 4.387A pdb=" N ASP B 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.808A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.964A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 324 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.828A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.936A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.969A pdb=" N ASN B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.926A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.686A pdb=" N GLN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.106A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.916A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 739 through 745 removed outlier: 3.692A pdb=" N GLU B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.849A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.656A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 10 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.656A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 10 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 93 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.706A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.346A 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 597 through 603 removed outlier: 3.748A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.539A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 736 removed outlier: 3.555A pdb=" N ILE A 733 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.747A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 73 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU C 87 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 71 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG C 89 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 69 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG C 91 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 67 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN C 93 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP C 65 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 45 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 removed outlier: 7.388A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.624A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 596 through 603 removed outlier: 3.505A pdb=" N ALA C 601 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 617 through 618 removed outlier: 3.740A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 732 through 736 removed outlier: 7.468A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.666A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.666A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 520 through 522 Processing sheet with id=AB9, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AC1, first strand: chain 'E' and resid 600 through 601 removed outlier: 3.989A pdb=" N ALA E 601 " --> pdb=" O THR E 608 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 608 " --> pdb=" O ALA E 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 732 through 736 removed outlier: 7.166A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.793A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 21 through 25 removed outlier: 7.337A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 21 through 25 removed outlier: 7.337A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.923A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU D 353 " --> pdb=" O ALA D 471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC8, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.595A pdb=" N GLY D 599 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.932A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.419A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.697A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.939A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N MET F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 87 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP F 65 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA F 48 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 379 through 380 removed outlier: 7.303A pdb=" N ILE F 379 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AD6, first strand: chain 'F' and resid 596 through 601 removed outlier: 6.584A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 735 through 736 removed outlier: 6.353A pdb=" N LEU F 735 " --> pdb=" O VAL F 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.578A pdb=" N PHE B 45 " --> pdb=" O PRO B 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AE1, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AE2, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AE3, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.580A pdb=" N PHE B 451 " --> pdb=" O TYR B 460 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 597 through 601 removed outlier: 4.095A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 614 through 615 removed outlier: 3.690A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 732 through 736 removed outlier: 7.071A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1582 hydrogen bonds defined for protein. 4575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12210 1.34 - 1.46: 4302 1.46 - 1.58: 20469 1.58 - 1.70: 16 1.70 - 1.81: 252 Bond restraints: 37249 Sorted by residual: bond pdb=" C ILE B 233 " pdb=" O ILE B 233 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.19e-02 7.06e+03 7.83e+01 bond pdb=" N ILE D 233 " pdb=" CA ILE D 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.07e-02 8.73e+03 1.21e+01 bond pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.36e+00 bond pdb=" N LEU D 237 " pdb=" CA LEU D 237 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.01e+00 bond pdb=" N GLU F 240 " pdb=" CA GLU F 240 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.26e-02 6.30e+03 8.86e+00 ... (remaining 37244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 49117 1.93 - 3.85: 1155 3.85 - 5.78: 186 5.78 - 7.70: 39 7.70 - 9.63: 8 Bond angle restraints: 50505 Sorted by residual: angle pdb=" N VAL C 605 " pdb=" CA VAL C 605 " pdb=" C VAL C 605 " ideal model delta sigma weight residual 111.91 106.23 5.68 8.90e-01 1.26e+00 4.07e+01 angle pdb=" N ILE D 233 " pdb=" CA ILE D 233 " pdb=" C ILE D 233 " ideal model delta sigma weight residual 113.10 108.01 5.09 9.70e-01 1.06e+00 2.75e+01 angle pdb=" C LYS B 235 " pdb=" CA LYS B 235 " pdb=" CB LYS B 235 " ideal model delta sigma weight residual 110.06 117.47 -7.41 1.44e+00 4.82e-01 2.65e+01 angle pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" O LEU B 243 " ideal model delta sigma weight residual 121.84 116.28 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N GLU B 247 " pdb=" CA GLU B 247 " pdb=" C GLU B 247 " ideal model delta sigma weight residual 111.96 105.39 6.57 1.41e+00 5.03e-01 2.17e+01 ... (remaining 50500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 22653 35.28 - 70.57: 278 70.57 - 105.85: 39 105.85 - 141.13: 7 141.13 - 176.42: 4 Dihedral angle restraints: 22981 sinusoidal: 9595 harmonic: 13386 Sorted by residual: dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 dihedral pdb=" CA ASP F 51 " pdb=" C ASP F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta harmonic sigma weight residual -180.00 -134.73 -45.27 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -142.33 -37.67 0 5.00e+00 4.00e-02 5.68e+01 ... (remaining 22978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4730 0.058 - 0.116: 904 0.116 - 0.173: 97 0.173 - 0.231: 9 0.231 - 0.289: 4 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CA ASP B 241 " pdb=" N ASP B 241 " pdb=" C ASP B 241 " pdb=" CB ASP B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU F 237 " pdb=" N LEU F 237 " pdb=" C LEU F 237 " pdb=" CB LEU F 237 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS B 235 " pdb=" N LYS B 235 " pdb=" C LYS B 235 " pdb=" CB LYS B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 5741 not shown) Planarity restraints: 6557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " 0.028 2.00e-02 2.50e+03 5.55e-02 3.09e+01 pdb=" C ILE B 233 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE B 233 " 0.034 2.00e-02 2.50e+03 pdb=" N GLN B 234 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 667 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 668 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 668 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 668 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.018 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B 602 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.003 2.00e-02 2.50e+03 ... (remaining 6554 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 452 2.64 - 3.20: 34235 3.20 - 3.77: 58156 3.77 - 4.33: 78455 4.33 - 4.90: 125675 Nonbonded interactions: 296973 Sorted by model distance: nonbonded pdb=" OG1 THR C 603 " pdb=" O GLY C 606 " model vdw 2.071 3.040 nonbonded pdb=" OE1 GLN C 277 " pdb=" OG1 THR C 284 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR E 603 " pdb=" O GLY E 606 " model vdw 2.128 3.040 nonbonded pdb=" OD1 ASP A 218 " pdb=" NH1 ARG D 198 " model vdw 2.129 3.120 nonbonded pdb=" OG1 THR F 603 " pdb=" O GLY F 606 " model vdw 2.141 3.040 ... (remaining 296968 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' and resid 2 through 774) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.200 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.003 0.105 37249 Z= 0.186 Angle : 0.698 9.627 50505 Z= 0.383 Chirality : 0.045 0.289 5744 Planarity : 0.005 0.104 6557 Dihedral : 13.368 176.416 14365 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 0.26 % Allowed : 0.41 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.13), residues: 4626 helix: 0.59 (0.12), residues: 1937 sheet: -2.16 (0.21), residues: 547 loop : -1.54 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 198 TYR 0.028 0.001 TYR F 63 PHE 0.012 0.001 PHE A 657 TRP 0.050 0.002 TRP B 602 HIS 0.005 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00320 (37249) covalent geometry : angle 0.69830 (50505) hydrogen bonds : bond 0.17835 ( 1567) hydrogen bonds : angle 7.01481 ( 4575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 426 time to evaluate : 1.665 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 217 MET cc_start: 0.6426 (tpt) cc_final: 0.5617 (mpp) REVERT: A 682 THR cc_start: 0.8254 (m) cc_final: 0.7980 (p) REVERT: C 425 ASP cc_start: 0.8830 (p0) cc_final: 0.8355 (p0) REVERT: C 473 THR cc_start: 0.8152 (m) cc_final: 0.7878 (p) REVERT: E 241 ASP cc_start: 0.2392 (OUTLIER) cc_final: 0.1345 (m-30) REVERT: E 243 LEU cc_start: 0.5995 (tp) cc_final: 0.5573 (mt) REVERT: E 512 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6368 (tpt90) REVERT: E 563 TRP cc_start: 0.5276 (p90) cc_final: 0.4328 (p90) REVERT: D 625 LEU cc_start: 0.7625 (mp) cc_final: 0.7275 (mp) REVERT: F 218 ASP cc_start: 0.7849 (m-30) cc_final: 0.7613 (p0) REVERT: F 427 MET cc_start: 0.3069 (mmp) cc_final: 0.2139 (mmp) REVERT: F 439 MET cc_start: 0.6887 (mtt) cc_final: 0.6662 (mtp) REVERT: F 496 MET cc_start: 0.7729 (tpt) cc_final: 0.7378 (tpt) REVERT: F 633 MET cc_start: 0.8264 (mpp) cc_final: 0.7708 (mpp) REVERT: B 171 TRP cc_start: 0.0010 (p90) cc_final: -0.0233 (p90) REVERT: B 245 ASP cc_start: 0.5926 (m-30) cc_final: 0.5712 (m-30) REVERT: B 386 ASP cc_start: 0.8497 (p0) cc_final: 0.7866 (p0) REVERT: B 476 THR cc_start: 0.8308 (t) cc_final: 0.7021 (m) outliers start: 10 outliers final: 4 residues processed: 435 average time/residue: 0.2252 time to fit residues: 164.6386 Evaluate side-chains 322 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 317 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 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: A 68 GLN A 73 GLN A 234 GLN A 310 HIS A 319 HIS C 83 GLN C 168 HIS ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN F 727 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.181421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.138168 restraints weight = 89971.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129474 restraints weight = 70965.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.129544 restraints weight = 60590.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.129449 restraints weight = 51716.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.129406 restraints weight = 45528.139| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 37249 Z= 0.235 Angle : 0.740 9.830 50505 Z= 0.370 Chirality : 0.047 0.214 5744 Planarity : 0.006 0.073 6557 Dihedral : 8.865 177.523 5172 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.26 % Rotamer: Outliers : 1.34 % Allowed : 8.83 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.12), residues: 4626 helix: 0.28 (0.12), residues: 2019 sheet: -2.13 (0.21), residues: 544 loop : -1.80 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 479 TYR 0.022 0.002 TYR A 493 PHE 0.024 0.002 PHE B 466 TRP 0.025 0.002 TRP B 602 HIS 0.010 0.002 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00528 (37249) covalent geometry : angle 0.74028 (50505) hydrogen bonds : bond 0.04514 ( 1567) hydrogen bonds : angle 5.53404 ( 4575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 351 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6352 (tpt) cc_final: 0.5409 (mpp) REVERT: A 237 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7644 (mm) REVERT: A 682 THR cc_start: 0.8674 (m) cc_final: 0.8346 (p) REVERT: A 698 MET cc_start: 0.2129 (mmt) cc_final: 0.1734 (mmt) REVERT: A 713 MET cc_start: 0.6893 (tmm) cc_final: 0.6592 (tmm) REVERT: C 735 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 241 ASP cc_start: 0.1066 (OUTLIER) cc_final: 0.0009 (m-30) REVERT: E 563 TRP cc_start: 0.5595 (p90) cc_final: 0.4741 (p90) REVERT: D 133 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7251 (mt-10) REVERT: D 625 LEU cc_start: 0.7970 (mp) cc_final: 0.7608 (mp) REVERT: F 439 MET cc_start: 0.6879 (mtt) cc_final: 0.6653 (mtp) REVERT: F 633 MET cc_start: 0.8031 (mpp) cc_final: 0.7449 (mpp) REVERT: B 171 TRP cc_start: 0.1071 (p90) cc_final: 0.0210 (p90) REVERT: B 386 ASP cc_start: 0.8407 (p0) cc_final: 0.7779 (p0) outliers start: 52 outliers final: 34 residues processed: 381 average time/residue: 0.2230 time to fit residues: 143.9763 Evaluate side-chains 349 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 125 optimal weight: 0.6980 chunk 286 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 415 optimal weight: 0.9990 chunk 263 optimal weight: 0.2980 chunk 306 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 314 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN F 666 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.187499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.150737 restraints weight = 90146.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.142475 restraints weight = 77615.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.142843 restraints weight = 63810.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.142999 restraints weight = 48783.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143094 restraints weight = 44533.590| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37249 Z= 0.114 Angle : 0.615 8.904 50505 Z= 0.301 Chirality : 0.043 0.177 5744 Planarity : 0.005 0.073 6557 Dihedral : 8.340 174.220 5168 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.84 % Favored : 94.14 % Rotamer: Outliers : 1.00 % Allowed : 11.76 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.13), residues: 4626 helix: 0.69 (0.12), residues: 2005 sheet: -1.92 (0.21), residues: 557 loop : -1.60 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 479 TYR 0.024 0.001 TYR D 332 PHE 0.015 0.001 PHE F 657 TRP 0.029 0.001 TRP A 563 HIS 0.005 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00251 (37249) covalent geometry : angle 0.61482 (50505) hydrogen bonds : bond 0.03686 ( 1567) hydrogen bonds : angle 4.92826 ( 4575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 359 time to evaluate : 1.496 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 217 MET cc_start: 0.6137 (tpt) cc_final: 0.5198 (mpp) REVERT: A 682 THR cc_start: 0.8518 (m) cc_final: 0.8088 (p) REVERT: A 713 MET cc_start: 0.7055 (tmm) cc_final: 0.6050 (tmm) REVERT: A 723 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5842 (mt) REVERT: C 440 LEU cc_start: 0.7963 (tp) cc_final: 0.7666 (mt) REVERT: C 702 MET cc_start: 0.7794 (mpp) cc_final: 0.7582 (mpp) REVERT: C 735 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7772 (mp) REVERT: E 241 ASP cc_start: 0.0552 (OUTLIER) cc_final: -0.0794 (m-30) REVERT: E 422 ASP cc_start: 0.6991 (m-30) cc_final: 0.6394 (m-30) REVERT: E 563 TRP cc_start: 0.5367 (p90) cc_final: 0.4757 (p90) REVERT: E 620 SER cc_start: 0.7807 (m) cc_final: 0.7316 (t) REVERT: D 133 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7146 (mt-10) REVERT: D 228 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 625 LEU cc_start: 0.7910 (mp) cc_final: 0.7586 (mp) REVERT: F 427 MET cc_start: 0.3170 (mmp) cc_final: 0.2210 (mmp) REVERT: F 633 MET cc_start: 0.7763 (mpp) cc_final: 0.7319 (mpp) REVERT: B 171 TRP cc_start: 0.1478 (p90) cc_final: 0.0380 (p90) REVERT: B 386 ASP cc_start: 0.8168 (p0) cc_final: 0.7585 (p0) REVERT: B 702 MET cc_start: 0.7078 (ptp) cc_final: 0.6510 (ptp) outliers start: 39 outliers final: 20 residues processed: 380 average time/residue: 0.2184 time to fit residues: 141.5400 Evaluate side-chains 354 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 253 optimal weight: 9.9990 chunk 257 optimal weight: 30.0000 chunk 457 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 210 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 340 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS D 18 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.178841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.144537 restraints weight = 88130.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.139598 restraints weight = 81919.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.139474 restraints weight = 66770.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.139113 restraints weight = 47969.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.139195 restraints weight = 46290.240| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 37249 Z= 0.303 Angle : 0.804 11.873 50505 Z= 0.400 Chirality : 0.048 0.295 5744 Planarity : 0.006 0.074 6557 Dihedral : 8.800 177.260 5166 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.71 % Favored : 91.27 % Rotamer: Outliers : 2.80 % Allowed : 13.41 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.12), residues: 4626 helix: 0.15 (0.11), residues: 2047 sheet: -2.30 (0.21), residues: 556 loop : -1.88 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 222 TYR 0.041 0.002 TYR A 493 PHE 0.038 0.003 PHE F 557 TRP 0.030 0.002 TRP B 563 HIS 0.013 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00681 (37249) covalent geometry : angle 0.80429 (50505) hydrogen bonds : bond 0.04582 ( 1567) hydrogen bonds : angle 5.43659 ( 4575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.0123 (OUTLIER) cc_final: -0.0249 (pm20) REVERT: A 217 MET cc_start: 0.5826 (tpt) cc_final: 0.4965 (mpp) REVERT: A 416 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6666 (p0) REVERT: A 451 PHE cc_start: 0.7469 (t80) cc_final: 0.7157 (t80) REVERT: A 698 MET cc_start: 0.2600 (mmt) cc_final: 0.2013 (mmt) REVERT: A 713 MET cc_start: 0.7336 (tmm) cc_final: 0.6382 (tmm) REVERT: C 230 MET cc_start: 0.5829 (mpp) cc_final: 0.5436 (mpp) REVERT: C 528 LEU cc_start: 0.8598 (pp) cc_final: 0.8218 (tt) REVERT: C 733 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7490 (mm) REVERT: C 735 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8017 (mp) REVERT: E 563 TRP cc_start: 0.5442 (p90) cc_final: 0.4617 (p90) REVERT: D 228 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 683 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7628 (ttm) REVERT: F 75 MET cc_start: 0.3838 (tmm) cc_final: 0.3326 (tmm) REVERT: F 220 ASN cc_start: 0.7009 (m110) cc_final: 0.6752 (m-40) REVERT: F 427 MET cc_start: 0.3862 (mmp) cc_final: 0.3649 (mmp) REVERT: F 431 TRP cc_start: 0.5472 (p90) cc_final: 0.4716 (t-100) REVERT: B 75 MET cc_start: 0.4641 (ppp) cc_final: 0.4347 (ppp) REVERT: B 375 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7402 (ptpt) REVERT: B 386 ASP cc_start: 0.8161 (p0) cc_final: 0.7630 (p0) REVERT: B 531 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8314 (mm) REVERT: B 533 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6546 (mm-30) outliers start: 109 outliers final: 66 residues processed: 389 average time/residue: 0.2163 time to fit residues: 143.2667 Evaluate side-chains 374 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 300 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 231 optimal weight: 40.0000 chunk 441 optimal weight: 0.0040 chunk 174 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 326 optimal weight: 50.0000 chunk 435 optimal weight: 0.7980 chunk 172 optimal weight: 50.0000 chunk 209 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 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 = 0.4678 r_free = 0.4678 target = 0.189055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.159348 restraints weight = 112529.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.152261 restraints weight = 103976.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152644 restraints weight = 111425.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152811 restraints weight = 85986.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.153848 restraints weight = 79199.836| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37249 Z= 0.199 Angle : 0.698 11.175 50505 Z= 0.343 Chirality : 0.045 0.241 5744 Planarity : 0.005 0.074 6557 Dihedral : 8.615 172.662 5164 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.59 % Favored : 92.39 % Rotamer: Outliers : 2.90 % Allowed : 14.82 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.12), residues: 4626 helix: 0.35 (0.12), residues: 2028 sheet: -2.23 (0.21), residues: 544 loop : -1.86 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 222 TYR 0.029 0.002 TYR A 493 PHE 0.020 0.002 PHE B 466 TRP 0.026 0.002 TRP F 558 HIS 0.018 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00450 (37249) covalent geometry : angle 0.69759 (50505) hydrogen bonds : bond 0.03961 ( 1567) hydrogen bonds : angle 5.13672 ( 4575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 317 time to evaluate : 1.518 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 85 MET cc_start: 0.2101 (ppp) cc_final: 0.1882 (ppp) REVERT: A 217 MET cc_start: 0.6296 (tpt) cc_final: 0.5302 (mpp) REVERT: A 416 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6549 (p0) REVERT: A 451 PHE cc_start: 0.7463 (t80) cc_final: 0.7137 (t80) REVERT: A 713 MET cc_start: 0.7228 (tmm) cc_final: 0.6287 (tmm) REVERT: A 723 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.5810 (mt) REVERT: C 230 MET cc_start: 0.5645 (mpp) cc_final: 0.5262 (mpp) REVERT: C 735 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8106 (mp) REVERT: E 273 LEU cc_start: 0.8241 (mt) cc_final: 0.7822 (mt) REVERT: E 563 TRP cc_start: 0.5681 (p90) cc_final: 0.4387 (p90) REVERT: D 228 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 409 MET cc_start: 0.7841 (tpt) cc_final: 0.7571 (tpt) REVERT: D 683 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7441 (ttm) REVERT: D 698 MET cc_start: 0.5109 (mmm) cc_final: 0.4744 (mmm) REVERT: F 220 ASN cc_start: 0.7097 (m110) cc_final: 0.6869 (m110) REVERT: F 431 TRP cc_start: 0.5603 (p90) cc_final: 0.4832 (t-100) REVERT: F 641 LEU cc_start: 0.8548 (mt) cc_final: 0.8240 (mt) REVERT: B 375 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7493 (ptpt) REVERT: B 386 ASP cc_start: 0.8432 (p0) cc_final: 0.7795 (p0) outliers start: 113 outliers final: 74 residues processed: 396 average time/residue: 0.2166 time to fit residues: 146.4454 Evaluate side-chains 375 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 296 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 317 optimal weight: 8.9990 chunk 274 optimal weight: 20.0000 chunk 286 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 409 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 291 optimal weight: 0.2980 chunk 135 optimal weight: 6.9990 chunk 337 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 157 optimal weight: 50.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.190648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161489 restraints weight = 113181.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.154709 restraints weight = 100380.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.155583 restraints weight = 112380.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155761 restraints weight = 83870.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.156782 restraints weight = 77514.902| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37249 Z= 0.144 Angle : 0.652 11.046 50505 Z= 0.316 Chirality : 0.044 0.243 5744 Planarity : 0.005 0.076 6557 Dihedral : 8.390 169.465 5164 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 2.44 % Allowed : 15.72 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.15 (0.13), residues: 4626 helix: 0.58 (0.12), residues: 2030 sheet: -2.03 (0.21), residues: 551 loop : -1.77 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 222 TYR 0.021 0.001 TYR A 493 PHE 0.043 0.001 PHE F 557 TRP 0.017 0.001 TRP B 563 HIS 0.005 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00327 (37249) covalent geometry : angle 0.65159 (50505) hydrogen bonds : bond 0.03600 ( 1567) hydrogen bonds : angle 4.89140 ( 4575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 322 time to evaluate : 1.519 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 217 MET cc_start: 0.6254 (tpt) cc_final: 0.5278 (mpp) REVERT: A 416 ASN cc_start: 0.6596 (OUTLIER) cc_final: 0.6393 (p0) REVERT: A 451 PHE cc_start: 0.7344 (t80) cc_final: 0.7049 (t80) REVERT: A 713 MET cc_start: 0.7219 (tmm) cc_final: 0.6309 (tmm) REVERT: A 723 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5559 (mt) REVERT: C 230 MET cc_start: 0.5693 (mpp) cc_final: 0.5277 (mpp) REVERT: C 512 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7749 (ptp90) REVERT: C 645 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7269 (mtt-85) REVERT: C 733 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7288 (mm) REVERT: C 735 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8038 (mp) REVERT: E 273 LEU cc_start: 0.8223 (mt) cc_final: 0.7806 (mt) REVERT: E 563 TRP cc_start: 0.5568 (p90) cc_final: 0.4649 (p90) REVERT: D 228 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 427 MET cc_start: 0.8349 (mtp) cc_final: 0.8071 (mtp) REVERT: D 683 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7486 (ttm) REVERT: D 698 MET cc_start: 0.5029 (mmm) cc_final: 0.4638 (mmm) REVERT: F 75 MET cc_start: 0.4130 (tmm) cc_final: 0.3671 (tmm) REVERT: F 220 ASN cc_start: 0.7064 (m110) cc_final: 0.6840 (m110) REVERT: F 431 TRP cc_start: 0.5691 (p90) cc_final: 0.4921 (t-100) REVERT: F 485 MET cc_start: 0.6726 (mmm) cc_final: 0.6444 (mmp) REVERT: F 558 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.6936 (m100) REVERT: B 386 ASP cc_start: 0.8330 (p0) cc_final: 0.7745 (p0) outliers start: 95 outliers final: 69 residues processed: 387 average time/residue: 0.2198 time to fit residues: 144.0641 Evaluate side-chains 381 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 304 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 151 optimal weight: 0.1980 chunk 184 optimal weight: 0.0000 chunk 226 optimal weight: 4.9990 chunk 450 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 446 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS F 18 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.185624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.138844 restraints weight = 90167.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.130789 restraints weight = 73345.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.132255 restraints weight = 63254.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.131251 restraints weight = 57131.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.131238 restraints weight = 53112.180| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37249 Z= 0.122 Angle : 0.637 10.680 50505 Z= 0.308 Chirality : 0.043 0.231 5744 Planarity : 0.005 0.073 6557 Dihedral : 8.187 166.660 5164 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.55 % Favored : 93.43 % Rotamer: Outliers : 2.39 % Allowed : 16.20 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.97 (0.13), residues: 4626 helix: 0.76 (0.12), residues: 2015 sheet: -1.95 (0.21), residues: 570 loop : -1.68 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 143 TYR 0.025 0.001 TYR D 332 PHE 0.016 0.001 PHE F 657 TRP 0.014 0.001 TRP F 558 HIS 0.005 0.001 HIS E 664 Details of bonding type rmsd covalent geometry : bond 0.00275 (37249) covalent geometry : angle 0.63670 (50505) hydrogen bonds : bond 0.03413 ( 1567) hydrogen bonds : angle 4.71293 ( 4575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 321 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6335 (tpt) cc_final: 0.5505 (mpp) REVERT: A 416 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6552 (p0) REVERT: A 451 PHE cc_start: 0.7805 (t80) cc_final: 0.7558 (t80) REVERT: A 682 THR cc_start: 0.8642 (m) cc_final: 0.8356 (p) REVERT: A 713 MET cc_start: 0.6808 (tmm) cc_final: 0.5936 (tmm) REVERT: A 723 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6340 (mt) REVERT: C 230 MET cc_start: 0.5346 (mpp) cc_final: 0.4998 (mpp) REVERT: C 446 GLU cc_start: 0.7756 (pm20) cc_final: 0.7426 (pm20) REVERT: C 512 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7936 (ptp90) REVERT: C 645 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7376 (mtt-85) REVERT: C 735 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7712 (mp) REVERT: E 273 LEU cc_start: 0.8176 (mt) cc_final: 0.7893 (mt) REVERT: E 422 ASP cc_start: 0.7316 (m-30) cc_final: 0.6696 (m-30) REVERT: E 563 TRP cc_start: 0.5852 (p90) cc_final: 0.5139 (p90) REVERT: E 620 SER cc_start: 0.7746 (m) cc_final: 0.7376 (t) REVERT: D 228 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 683 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7516 (ttm) REVERT: D 698 MET cc_start: 0.5049 (mmm) cc_final: 0.4734 (mmm) REVERT: D 730 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7741 (tt) REVERT: F 63 TYR cc_start: 0.5787 (m-10) cc_final: 0.5390 (m-10) REVERT: F 431 TRP cc_start: 0.5603 (p90) cc_final: 0.5196 (t-100) REVERT: F 558 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.6648 (m100) REVERT: F 635 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: B 386 ASP cc_start: 0.8500 (p0) cc_final: 0.7780 (p0) outliers start: 93 outliers final: 61 residues processed: 385 average time/residue: 0.2201 time to fit residues: 143.8362 Evaluate side-chains 371 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 436 optimal weight: 7.9990 chunk 371 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 410 optimal weight: 0.0980 chunk 323 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 413 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 400 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 317 optimal weight: 0.0170 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 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 = 0.4700 r_free = 0.4700 target = 0.186984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.139301 restraints weight = 94335.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.133373 restraints weight = 77537.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133301 restraints weight = 75769.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.134986 restraints weight = 62716.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.133934 restraints weight = 52414.547| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37249 Z= 0.122 Angle : 0.643 10.063 50505 Z= 0.310 Chirality : 0.044 0.249 5744 Planarity : 0.005 0.068 6557 Dihedral : 8.086 165.266 5164 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.49 % Favored : 93.49 % Rotamer: Outliers : 2.16 % Allowed : 16.74 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.89 (0.13), residues: 4626 helix: 0.80 (0.12), residues: 2016 sheet: -1.84 (0.21), residues: 549 loop : -1.64 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 479 TYR 0.019 0.001 TYR F 224 PHE 0.009 0.001 PHE F 376 TRP 0.014 0.001 TRP F 558 HIS 0.005 0.001 HIS E 664 Details of bonding type rmsd covalent geometry : bond 0.00278 (37249) covalent geometry : angle 0.64287 (50505) hydrogen bonds : bond 0.03338 ( 1567) hydrogen bonds : angle 4.63241 ( 4575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 317 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6296 (tpt) cc_final: 0.5600 (mpp) REVERT: A 416 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6601 (p0) REVERT: A 451 PHE cc_start: 0.7870 (t80) cc_final: 0.7642 (t80) REVERT: A 682 THR cc_start: 0.8599 (m) cc_final: 0.8315 (p) REVERT: A 713 MET cc_start: 0.6610 (tmm) cc_final: 0.5819 (tmm) REVERT: A 723 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6236 (mt) REVERT: C 230 MET cc_start: 0.5412 (mpp) cc_final: 0.5093 (mpp) REVERT: C 735 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7623 (mp) REVERT: E 273 LEU cc_start: 0.8118 (mt) cc_final: 0.7859 (mt) REVERT: E 422 ASP cc_start: 0.7127 (m-30) cc_final: 0.6395 (m-30) REVERT: E 563 TRP cc_start: 0.5915 (p90) cc_final: 0.5324 (p90) REVERT: E 620 SER cc_start: 0.7865 (m) cc_final: 0.7572 (t) REVERT: D 228 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 683 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7231 (ttm) REVERT: D 698 MET cc_start: 0.4933 (mmm) cc_final: 0.4596 (mmm) REVERT: D 730 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7671 (tt) REVERT: F 431 TRP cc_start: 0.5556 (p90) cc_final: 0.5286 (t-100) REVERT: F 485 MET cc_start: 0.6690 (mmm) cc_final: 0.6451 (mmp) REVERT: F 558 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6641 (m100) REVERT: F 633 MET cc_start: 0.8423 (mpp) cc_final: 0.7735 (mpp) REVERT: F 635 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: B 386 ASP cc_start: 0.8497 (p0) cc_final: 0.7762 (p0) outliers start: 84 outliers final: 63 residues processed: 371 average time/residue: 0.2235 time to fit residues: 139.7398 Evaluate side-chains 375 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 316 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 239 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 365 optimal weight: 0.0870 chunk 213 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 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 = 0.4633 r_free = 0.4633 target = 0.180103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.132268 restraints weight = 87864.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.123521 restraints weight = 74350.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124733 restraints weight = 67422.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124233 restraints weight = 55574.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124122 restraints weight = 51254.324| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 37249 Z= 0.245 Angle : 0.761 11.650 50505 Z= 0.375 Chirality : 0.047 0.265 5744 Planarity : 0.006 0.064 6557 Dihedral : 8.513 166.704 5164 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 2.47 % Allowed : 17.00 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 4626 helix: 0.43 (0.12), residues: 2020 sheet: -2.04 (0.22), residues: 524 loop : -1.80 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 645 TYR 0.030 0.002 TYR C 658 PHE 0.035 0.002 PHE A 376 TRP 0.031 0.002 TRP B 563 HIS 0.010 0.002 HIS C 726 Details of bonding type rmsd covalent geometry : bond 0.00554 (37249) covalent geometry : angle 0.76122 (50505) hydrogen bonds : bond 0.04098 ( 1567) hydrogen bonds : angle 5.09669 ( 4575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 304 time to evaluate : 1.725 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 217 MET cc_start: 0.6356 (tpt) cc_final: 0.5572 (mpp) REVERT: A 416 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.7028 (p0) REVERT: A 451 PHE cc_start: 0.8067 (t80) cc_final: 0.7808 (t80) REVERT: A 713 MET cc_start: 0.6696 (tmm) cc_final: 0.5877 (tmm) REVERT: A 723 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6304 (mt) REVERT: C 230 MET cc_start: 0.5336 (mpp) cc_final: 0.4986 (mpp) REVERT: C 735 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7843 (mp) REVERT: E 273 LEU cc_start: 0.8136 (mt) cc_final: 0.7874 (mt) REVERT: E 543 LEU cc_start: 0.8236 (mt) cc_final: 0.7912 (tt) REVERT: E 563 TRP cc_start: 0.5710 (p90) cc_final: 0.4722 (p90) REVERT: D 683 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7609 (ttm) REVERT: D 730 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7877 (tt) REVERT: F 485 MET cc_start: 0.6845 (mmm) cc_final: 0.6510 (mmp) REVERT: F 521 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5340 (pm20) REVERT: F 558 TRP cc_start: 0.6956 (OUTLIER) cc_final: 0.6624 (m100) REVERT: B 375 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: B 386 ASP cc_start: 0.8449 (p0) cc_final: 0.7740 (p0) outliers start: 96 outliers final: 72 residues processed: 374 average time/residue: 0.2193 time to fit residues: 139.1352 Evaluate side-chains 374 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 376 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 326 optimal weight: 30.0000 chunk 319 optimal weight: 5.9990 chunk 435 optimal weight: 0.9990 chunk 344 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN E 664 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.184400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.136707 restraints weight = 87285.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.128578 restraints weight = 72860.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.129182 restraints weight = 61346.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.129148 restraints weight = 52573.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.129203 restraints weight = 48273.492| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37249 Z= 0.131 Angle : 0.677 14.708 50505 Z= 0.327 Chirality : 0.044 0.246 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.256 168.210 5164 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 17.69 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.02 (0.13), residues: 4626 helix: 0.69 (0.12), residues: 2014 sheet: -1.85 (0.22), residues: 528 loop : -1.73 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 503 TYR 0.051 0.001 TYR B 768 PHE 0.033 0.001 PHE A 376 TRP 0.015 0.001 TRP B 563 HIS 0.006 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00299 (37249) covalent geometry : angle 0.67701 (50505) hydrogen bonds : bond 0.03492 ( 1567) hydrogen bonds : angle 4.75157 ( 4575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 313 time to evaluate : 1.515 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 217 MET cc_start: 0.6394 (tpt) cc_final: 0.5523 (mpp) REVERT: A 416 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6690 (p0) REVERT: A 440 LEU cc_start: 0.7516 (tt) cc_final: 0.7253 (mt) REVERT: A 451 PHE cc_start: 0.7759 (t80) cc_final: 0.7504 (t80) REVERT: A 479 ARG cc_start: 0.5641 (ptt-90) cc_final: 0.5339 (ptt90) REVERT: A 682 THR cc_start: 0.8653 (m) cc_final: 0.8354 (p) REVERT: A 713 MET cc_start: 0.6930 (tmm) cc_final: 0.6020 (tmm) REVERT: A 723 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6130 (mt) REVERT: C 230 MET cc_start: 0.5505 (mpp) cc_final: 0.5126 (mpp) REVERT: C 735 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7679 (mp) REVERT: E 273 LEU cc_start: 0.8218 (mt) cc_final: 0.7953 (mt) REVERT: E 563 TRP cc_start: 0.5743 (p90) cc_final: 0.4775 (p90) REVERT: E 620 SER cc_start: 0.7947 (m) cc_final: 0.7642 (t) REVERT: D 683 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7384 (ttm) REVERT: D 730 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7785 (tt) REVERT: F 258 MET cc_start: 0.0526 (mmp) cc_final: -0.0912 (mtt) REVERT: F 485 MET cc_start: 0.6848 (mmm) cc_final: 0.6569 (mmp) REVERT: F 521 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5459 (pm20) REVERT: F 558 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6761 (m100) REVERT: F 635 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: B 386 ASP cc_start: 0.8398 (p0) cc_final: 0.7660 (p0) outliers start: 79 outliers final: 63 residues processed: 364 average time/residue: 0.2229 time to fit residues: 136.6424 Evaluate side-chains 378 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 635 GLU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 240 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 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 = 0.4625 r_free = 0.4625 target = 0.179260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.132900 restraints weight = 87791.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.124159 restraints weight = 72600.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124900 restraints weight = 61921.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124637 restraints weight = 52748.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124667 restraints weight = 49460.810| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 37249 Z= 0.270 Angle : 0.794 13.263 50505 Z= 0.391 Chirality : 0.048 0.284 5744 Planarity : 0.006 0.100 6557 Dihedral : 8.617 167.379 5164 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.82 % Favored : 91.16 % Rotamer: Outliers : 2.18 % Allowed : 17.75 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.12), residues: 4626 helix: 0.31 (0.12), residues: 2021 sheet: -2.18 (0.22), residues: 515 loop : -1.86 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 479 TYR 0.029 0.002 TYR A 493 PHE 0.031 0.002 PHE A 376 TRP 0.034 0.002 TRP B 563 HIS 0.011 0.002 HIS C 726 Details of bonding type rmsd covalent geometry : bond 0.00610 (37249) covalent geometry : angle 0.79426 (50505) hydrogen bonds : bond 0.04242 ( 1567) hydrogen bonds : angle 5.18511 ( 4575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8121.35 seconds wall clock time: 140 minutes 54.55 seconds (8454.55 seconds total)