Starting phenix.real_space_refine on Wed May 28 12:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypj_34002/05_2025/7ypj_34002.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 105 5.16 5 C 19230 2.51 5 N 5355 2.21 5 O 5780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.66s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30478 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.81, per 1000 atoms: 0.58 Number of scatterers: 30478 At special positions: 0 Unit cell: (168.699, 169.76, 188.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 8 15.00 O 5780 8.00 N 5355 7.00 C 19230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 3.7 seconds 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 36 sheets defined 48.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 4.288A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.548A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.592A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.764A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 235 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.860A pdb=" N ASP A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.594A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.588A pdb=" N LYS A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 5.017A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.553A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.658A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.561A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.873A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.854A pdb=" N LYS A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.808A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.879A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.855A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.633A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.783A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.604A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.922A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.710A pdb=" N GLN B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 removed outlier: 3.899A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 186 through 237 Processing helix chain 'B' and resid 239 through 256 removed outlier: 3.530A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.732A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.786A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.974A pdb=" N GLN B 411 " --> pdb=" O HIS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 444 removed outlier: 4.565A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 443 " --> pdb=" O MET B 439 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.625A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.602A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.856A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.714A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 727 Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'C' and resid 29 through 39 removed outlier: 5.045A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 Processing helix chain 'C' and resid 140 through 143 Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 157 through 169 removed outlier: 4.172A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 184 through 238 removed outlier: 3.732A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 256 removed outlier: 3.561A pdb=" N LEU C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.535A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 removed outlier: 3.928A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 506 through 515 removed outlier: 3.527A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 515 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.617A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.674A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 717 through 727 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.938A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.809A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.738A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.749A pdb=" N GLY D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 184 through 238 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.953A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.634A pdb=" N THR D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.636A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 386 through 391 removed outlier: 4.165A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.572A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.770A pdb=" N ASP D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 4.064A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.624A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 534 Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.905A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 586 through 590 removed outlier: 4.221A pdb=" N THR D 590 " --> pdb=" O LYS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 646 Processing helix chain 'D' and resid 647 through 651 removed outlier: 3.625A pdb=" N ASP D 650 " --> pdb=" O HIS D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'D' and resid 679 through 692 removed outlier: 4.099A pdb=" N MET D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.508A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 726 " --> pdb=" O LEU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 3.748A pdb=" N LEU D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 4.602A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 770 Processing helix chain 'E' and resid 27 through 39 removed outlier: 4.310A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 117 through 139 Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.508A pdb=" N ALA E 169 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.730A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 235 Processing helix chain 'E' and resid 237 through 245 Processing helix chain 'E' and resid 246 through 257 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 281 through 288 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.703A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.567A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'E' and resid 444 through 449 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.530A pdb=" N LEU E 481 " --> pdb=" O PRO E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 514 removed outlier: 3.511A pdb=" N ALA E 502 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 523 through 534 Processing helix chain 'E' and resid 543 through 561 removed outlier: 4.182A pdb=" N LEU E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY E 561 " --> pdb=" O PHE E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.578A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 589 removed outlier: 4.175A pdb=" N LYS E 587 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 651 removed outlier: 4.158A pdb=" N THR E 642 " --> pdb=" O GLN E 638 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 659 removed outlier: 3.514A pdb=" N PHE E 657 " --> pdb=" O PRO E 654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 659 " --> pdb=" O ASP E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 693 removed outlier: 4.019A pdb=" N ALA E 684 " --> pdb=" O GLY E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 729 removed outlier: 3.578A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 738 No H-bonds generated for 'chain 'E' and resid 736 through 738' Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.379A pdb=" N GLU E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 770 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.731A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 71 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG A 89 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA A 69 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 91 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 67 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 93 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP A 65 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.731A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A 106 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR A 97 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 104 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.516A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.453A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.576A pdb=" N VAL A 665 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.853A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 20 through 25 removed outlier: 7.836A pdb=" N LEU B 82 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 379 removed outlier: 6.356A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 598 through 603 removed outlier: 3.655A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 614 Processing sheet with id=AB2, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.616A pdb=" N VAL B 734 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.713A pdb=" N LEU C 5 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.725A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.725A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C 83 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.413A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP C 422 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 520 through 522 Processing sheet with id=AC1, first strand: chain 'C' and resid 592 through 593 Processing sheet with id=AC2, first strand: chain 'C' and resid 624 through 625 removed outlier: 5.923A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 705 through 707 removed outlier: 4.146A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.587A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE D 98 " --> pdb=" O ARG D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.535A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLN D 83 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA D 74 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 72 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.535A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 91 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AC8, first strand: chain 'D' and resid 377 through 378 removed outlier: 3.727A pdb=" N HIS D 377 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.779A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 617 through 618 removed outlier: 3.563A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL D 665 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 617 through 618 removed outlier: 3.563A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR D 608 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N MET D 702 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN D 598 " --> pdb=" O MET D 702 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.869A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP E 96 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 108 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL E 94 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 110 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 92 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.869A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP E 96 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 108 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL E 94 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 110 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 92 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 352 through 353 removed outlier: 7.682A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.832A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 468 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 421 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.049A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 732 through 733 1299 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.22 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5772 1.32 - 1.45: 7324 1.45 - 1.58: 17713 1.58 - 1.70: 12 1.70 - 1.83: 210 Bond restraints: 31031 Sorted by residual: bond pdb=" C GLN E 229 " pdb=" O GLN E 229 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.78e+01 bond pdb=" CB MET D 427 " pdb=" CG MET D 427 " ideal model delta sigma weight residual 1.520 1.415 0.105 3.00e-02 1.11e+03 1.24e+01 bond pdb=" N ILE D 681 " pdb=" CA ILE D 681 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.26e-02 6.30e+03 9.09e+00 bond pdb=" N VAL A 54 " pdb=" CA VAL A 54 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.95e+00 bond pdb=" CA LEU C 421 " pdb=" CB LEU C 421 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.53e-02 4.27e+03 8.91e+00 ... (remaining 31026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 41099 3.58 - 7.16: 878 7.16 - 10.73: 83 10.73 - 14.31: 11 14.31 - 17.89: 4 Bond angle restraints: 42075 Sorted by residual: angle pdb=" CA PRO A 714 " pdb=" N PRO A 714 " pdb=" CD PRO A 714 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 angle pdb=" N GLY E 358 " pdb=" CA GLY E 358 " pdb=" C GLY E 358 " ideal model delta sigma weight residual 113.99 121.13 -7.14 1.28e+00 6.10e-01 3.11e+01 angle pdb=" N GLN E 229 " pdb=" CA GLN E 229 " pdb=" C GLN E 229 " ideal model delta sigma weight residual 110.97 104.97 6.00 1.09e+00 8.42e-01 3.03e+01 angle pdb=" C ALA A 400 " pdb=" N MET A 401 " pdb=" CA MET A 401 " ideal model delta sigma weight residual 122.90 111.57 11.33 2.07e+00 2.33e-01 2.99e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 107.70 101.40 6.30 1.22e+00 6.72e-01 2.66e+01 ... (remaining 42070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.63: 18706 30.63 - 61.25: 393 61.25 - 91.88: 42 91.88 - 122.50: 0 122.50 - 153.13: 3 Dihedral angle restraints: 19144 sinusoidal: 7989 harmonic: 11155 Sorted by residual: dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 146.88 153.13 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 164.64 135.35 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O2A ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PA ADP C 801 " pdb=" PB ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 172.24 127.76 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 19141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4352 0.110 - 0.221: 404 0.221 - 0.331: 28 0.331 - 0.442: 1 0.442 - 0.552: 1 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CG LEU C 629 " pdb=" CB LEU C 629 " pdb=" CD1 LEU C 629 " pdb=" CD2 LEU C 629 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CG LEU A 751 " pdb=" CB LEU A 751 " pdb=" CD1 LEU A 751 " pdb=" CD2 LEU A 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CG LEU C 722 " pdb=" CB LEU C 722 " pdb=" CD1 LEU C 722 " pdb=" CD2 LEU C 722 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 4783 not shown) Planarity restraints: 5464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 713 " 0.069 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 714 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 714 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 714 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 171 " -0.023 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP E 171 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP E 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 171 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 171 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP E 171 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 171 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 171 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 171 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 228 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLU E 228 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 228 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 229 " -0.019 2.00e-02 2.50e+03 ... (remaining 5461 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1993 2.71 - 3.26: 32599 3.26 - 3.81: 54300 3.81 - 4.35: 67257 4.35 - 4.90: 104778 Nonbonded interactions: 260927 Sorted by model distance: nonbonded pdb=" O ALA D 639 " pdb=" OG1 THR D 642 " model vdw 2.167 3.040 nonbonded pdb=" O LEU D 528 " pdb=" OG SER D 532 " model vdw 2.177 3.040 nonbonded pdb=" O LEU D 364 " pdb=" OG SER D 367 " model vdw 2.185 3.040 nonbonded pdb=" O MET A 160 " pdb=" OG1 THR A 164 " model vdw 2.194 3.040 nonbonded pdb=" O ALA A 678 " pdb=" OG1 THR A 703 " model vdw 2.201 3.040 ... (remaining 260922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) selection = (chain 'D' and resid 2 through 774) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 68.510 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 31031 Z= 0.398 Angle : 1.265 17.891 42075 Z= 0.708 Chirality : 0.066 0.552 4786 Planarity : 0.008 0.098 5464 Dihedral : 13.225 153.127 11964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 0.12 % Allowed : 1.08 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.12), residues: 3855 helix: -1.16 (0.12), residues: 1615 sheet: -2.43 (0.25), residues: 360 loop : -2.40 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP E 171 HIS 0.016 0.003 HIS B 407 PHE 0.050 0.003 PHE E 467 TYR 0.036 0.003 TYR C 460 ARG 0.030 0.001 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.19258 ( 1287) hydrogen bonds : angle 8.11545 ( 3756) covalent geometry : bond 0.00786 (31031) covalent geometry : angle 1.26486 (42075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8354 (mmp) cc_final: 0.7993 (mmm) REVERT: A 698 MET cc_start: 0.4634 (mtt) cc_final: 0.3780 (mtt) REVERT: B 230 MET cc_start: 0.8760 (ttp) cc_final: 0.8456 (ppp) REVERT: B 351 LEU cc_start: 0.9292 (tp) cc_final: 0.9067 (tp) REVERT: B 379 ILE cc_start: 0.9565 (tp) cc_final: 0.9250 (tt) REVERT: B 409 MET cc_start: 0.9057 (tpt) cc_final: 0.8479 (tpp) REVERT: C 422 ASP cc_start: 0.8557 (t70) cc_final: 0.8338 (t0) REVERT: C 476 THR cc_start: 0.8976 (t) cc_final: 0.8743 (p) REVERT: C 483 ASP cc_start: 0.8804 (p0) cc_final: 0.8536 (p0) REVERT: C 711 LYS cc_start: 0.8909 (mptt) cc_final: 0.8680 (mmmt) REVERT: D 230 MET cc_start: 0.8295 (tmm) cc_final: 0.7813 (tmm) REVERT: D 317 GLU cc_start: 0.8345 (pp20) cc_final: 0.8084 (pp20) REVERT: D 401 MET cc_start: 0.9120 (ttp) cc_final: 0.8899 (pmm) REVERT: D 713 MET cc_start: 0.8723 (tpt) cc_final: 0.8471 (tpp) REVERT: E 255 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: E 657 PHE cc_start: 0.9066 (t80) cc_final: 0.8640 (t80) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.4342 time to fit residues: 153.3381 Evaluate side-chains 175 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 40.0000 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.088313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.065579 restraints weight = 142960.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.065579 restraints weight = 153684.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.065579 restraints weight = 153663.326| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31031 Z= 0.182 Angle : 0.755 12.208 42075 Z= 0.381 Chirality : 0.046 0.233 4786 Planarity : 0.006 0.063 5464 Dihedral : 7.744 137.604 4304 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.62 % Allowed : 7.10 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.13), residues: 3855 helix: -0.50 (0.12), residues: 1652 sheet: -2.42 (0.26), residues: 354 loop : -2.28 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 171 HIS 0.007 0.001 HIS B 407 PHE 0.016 0.001 PHE E 467 TYR 0.025 0.002 TYR D 643 ARG 0.007 0.001 ARG E 395 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1287) hydrogen bonds : angle 6.04592 ( 3756) covalent geometry : bond 0.00363 (31031) covalent geometry : angle 0.75539 (42075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 3.217 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 49 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.4462 (pm20) REVERT: A 85 MET cc_start: 0.8127 (mmp) cc_final: 0.7749 (mmm) REVERT: B 379 ILE cc_start: 0.9490 (tp) cc_final: 0.9271 (tt) REVERT: B 427 MET cc_start: 0.7848 (mmp) cc_final: 0.7561 (mmt) REVERT: C 75 MET cc_start: 0.2152 (tmm) cc_final: 0.1939 (tmm) REVERT: C 258 MET cc_start: 0.3597 (mtt) cc_final: 0.3270 (mtt) REVERT: C 476 THR cc_start: 0.8693 (t) cc_final: 0.8452 (p) REVERT: C 483 ASP cc_start: 0.8462 (p0) cc_final: 0.8232 (p0) REVERT: D 437 SER cc_start: 0.9671 (m) cc_final: 0.9453 (p) REVERT: D 516 MET cc_start: 0.7595 (ttm) cc_final: 0.6369 (mmm) REVERT: D 727 GLN cc_start: 0.5158 (OUTLIER) cc_final: 0.4833 (mm-40) REVERT: E 85 MET cc_start: 0.6674 (mpp) cc_final: 0.6242 (mpp) REVERT: E 657 PHE cc_start: 0.9106 (t80) cc_final: 0.8688 (t80) outliers start: 20 outliers final: 10 residues processed: 190 average time/residue: 0.3864 time to fit residues: 122.9615 Evaluate side-chains 176 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 204 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 284 optimal weight: 0.1980 chunk 117 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 313 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN E 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.100889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.072259 restraints weight = 285233.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.070866 restraints weight = 239131.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.070715 restraints weight = 190307.675| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31031 Z= 0.151 Angle : 0.699 12.340 42075 Z= 0.347 Chirality : 0.044 0.179 4786 Planarity : 0.005 0.059 5464 Dihedral : 7.345 134.080 4302 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.23 % Allowed : 9.63 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3855 helix: -0.07 (0.13), residues: 1643 sheet: -2.33 (0.25), residues: 378 loop : -2.09 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 602 HIS 0.005 0.001 HIS E 377 PHE 0.011 0.001 PHE E 467 TYR 0.019 0.002 TYR E 224 ARG 0.004 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 1287) hydrogen bonds : angle 5.60813 ( 3756) covalent geometry : bond 0.00317 (31031) covalent geometry : angle 0.69927 (42075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 3.293 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 496 MET cc_start: 0.8569 (mmp) cc_final: 0.8222 (mmp) REVERT: B 230 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7964 (ppp) REVERT: B 633 MET cc_start: 0.8602 (mmm) cc_final: 0.8392 (mmm) REVERT: C 258 MET cc_start: 0.3355 (mtt) cc_final: 0.3066 (mtt) REVERT: C 439 MET cc_start: 0.9437 (mmm) cc_final: 0.9082 (mmm) REVERT: C 483 ASP cc_start: 0.8489 (p0) cc_final: 0.8196 (p0) REVERT: C 501 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8041 (tt) REVERT: C 516 MET cc_start: 0.7386 (tmm) cc_final: 0.7180 (tmm) REVERT: D 160 MET cc_start: 0.1162 (OUTLIER) cc_final: 0.0404 (ppp) REVERT: D 230 MET cc_start: 0.8113 (tmm) cc_final: 0.7841 (tmm) REVERT: D 317 GLU cc_start: 0.8067 (pp20) cc_final: 0.7812 (pp20) REVERT: D 437 SER cc_start: 0.9512 (m) cc_final: 0.9256 (p) REVERT: D 499 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: D 516 MET cc_start: 0.7088 (ttm) cc_final: 0.6062 (mmm) REVERT: D 713 MET cc_start: 0.8185 (tpp) cc_final: 0.7788 (tpp) REVERT: D 727 GLN cc_start: 0.5063 (OUTLIER) cc_final: 0.4831 (mm-40) REVERT: E 427 MET cc_start: 0.8267 (mmm) cc_final: 0.7967 (mmm) REVERT: E 657 PHE cc_start: 0.9035 (t80) cc_final: 0.8499 (t80) outliers start: 40 outliers final: 9 residues processed: 208 average time/residue: 0.3896 time to fit residues: 135.6865 Evaluate side-chains 182 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 250 optimal weight: 50.0000 chunk 343 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 251 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 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 = 0.4310 r_free = 0.4310 target = 0.082847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.059087 restraints weight = 154297.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.059092 restraints weight = 153166.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.059092 restraints weight = 152976.755| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31031 Z= 0.298 Angle : 0.838 13.091 42075 Z= 0.426 Chirality : 0.047 0.216 4786 Planarity : 0.006 0.063 5464 Dihedral : 7.653 133.042 4302 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.73 % Allowed : 11.85 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3855 helix: -0.34 (0.12), residues: 1669 sheet: -2.26 (0.26), residues: 371 loop : -2.15 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 298 HIS 0.010 0.002 HIS C 319 PHE 0.017 0.002 PHE C 466 TYR 0.036 0.002 TYR D 643 ARG 0.008 0.001 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 1287) hydrogen bonds : angle 5.92078 ( 3756) covalent geometry : bond 0.00605 (31031) covalent geometry : angle 0.83798 (42075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.5397 (pm20) REVERT: A 427 MET cc_start: 0.5092 (tpt) cc_final: 0.4782 (tpt) REVERT: A 496 MET cc_start: 0.8609 (mmp) cc_final: 0.8224 (mmp) REVERT: B 439 MET cc_start: 0.9105 (tmm) cc_final: 0.8873 (ppp) REVERT: B 633 MET cc_start: 0.8957 (mmm) cc_final: 0.8433 (mmt) REVERT: C 439 MET cc_start: 0.9798 (mmm) cc_final: 0.9534 (mmm) REVERT: C 756 ILE cc_start: 0.2372 (OUTLIER) cc_final: 0.2122 (mm) REVERT: D 160 MET cc_start: 0.1553 (mmp) cc_final: 0.0637 (ppp) REVERT: D 713 MET cc_start: 0.8855 (tpp) cc_final: 0.8342 (tpp) REVERT: E 276 MET cc_start: 0.5096 (mmp) cc_final: 0.4859 (mmm) REVERT: E 657 PHE cc_start: 0.9015 (t80) cc_final: 0.8655 (t80) outliers start: 56 outliers final: 31 residues processed: 208 average time/residue: 0.4066 time to fit residues: 140.9646 Evaluate side-chains 190 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 71 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 381 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 333 optimal weight: 8.9990 chunk 332 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 373 ASN ** E 666 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 = 0.4317 r_free = 0.4317 target = 0.083372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.059312 restraints weight = 151211.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.059388 restraints weight = 151758.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.059388 restraints weight = 149241.614| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31031 Z= 0.232 Angle : 0.783 13.095 42075 Z= 0.393 Chirality : 0.046 0.257 4786 Planarity : 0.006 0.055 5464 Dihedral : 7.580 133.186 4302 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.16 % Allowed : 13.49 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3855 helix: -0.27 (0.13), residues: 1668 sheet: -2.12 (0.26), residues: 364 loop : -2.14 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 298 HIS 0.008 0.002 HIS E 377 PHE 0.015 0.002 PHE D 467 TYR 0.028 0.002 TYR D 643 ARG 0.006 0.001 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 1287) hydrogen bonds : angle 5.75500 ( 3756) covalent geometry : bond 0.00482 (31031) covalent geometry : angle 0.78275 (42075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 169 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4854 (tpt) cc_final: 0.4528 (tpt) REVERT: A 496 MET cc_start: 0.8526 (mmp) cc_final: 0.8111 (mmp) REVERT: A 698 MET cc_start: 0.3789 (mtt) cc_final: 0.2682 (mtt) REVERT: B 439 MET cc_start: 0.8893 (tmm) cc_final: 0.8591 (tmm) REVERT: B 472 ASN cc_start: 0.9548 (t0) cc_final: 0.9179 (p0) REVERT: B 567 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6905 (mtt-85) REVERT: B 600 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5872 (pp) REVERT: B 633 MET cc_start: 0.9156 (mmm) cc_final: 0.8648 (mmt) REVERT: C 439 MET cc_start: 0.9793 (mmm) cc_final: 0.9536 (mmm) REVERT: C 756 ILE cc_start: 0.3163 (OUTLIER) cc_final: 0.2777 (mm) REVERT: D 160 MET cc_start: 0.1541 (OUTLIER) cc_final: 0.0610 (ppp) REVERT: D 230 MET cc_start: 0.8317 (tmm) cc_final: 0.8081 (tmm) REVERT: D 713 MET cc_start: 0.8814 (tpp) cc_final: 0.8340 (tpp) REVERT: E 256 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.4543 (t) REVERT: E 276 MET cc_start: 0.5163 (mmp) cc_final: 0.4897 (mmm) REVERT: E 372 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.4348 (tpp) REVERT: E 657 PHE cc_start: 0.8985 (t80) cc_final: 0.8597 (t80) outliers start: 70 outliers final: 32 residues processed: 228 average time/residue: 0.3925 time to fit residues: 150.9903 Evaluate side-chains 200 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 164 optimal weight: 50.0000 chunk 167 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 GLN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 666 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 = 0.4295 r_free = 0.4295 target = 0.096027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.066853 restraints weight = 288662.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.065310 restraints weight = 234433.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.065993 restraints weight = 190874.465| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 31031 Z= 0.296 Angle : 0.867 11.319 42075 Z= 0.436 Chirality : 0.048 0.241 4786 Planarity : 0.006 0.061 5464 Dihedral : 7.722 133.352 4299 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3855 helix: -0.49 (0.12), residues: 1671 sheet: -2.11 (0.27), residues: 351 loop : -2.21 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 298 HIS 0.010 0.002 HIS E 454 PHE 0.015 0.002 PHE D 467 TYR 0.036 0.002 TYR D 643 ARG 0.009 0.001 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 1287) hydrogen bonds : angle 5.98740 ( 3756) covalent geometry : bond 0.00614 (31031) covalent geometry : angle 0.86673 (42075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4894 (tpt) cc_final: 0.4388 (tpt) REVERT: A 496 MET cc_start: 0.8696 (mmp) cc_final: 0.8357 (mmp) REVERT: A 625 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8994 (tp) REVERT: A 698 MET cc_start: 0.3796 (mtt) cc_final: 0.3313 (mtt) REVERT: B 516 MET cc_start: 0.8051 (tpp) cc_final: 0.7671 (tpp) REVERT: B 567 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7058 (mtt-85) REVERT: B 600 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6307 (pp) REVERT: C 439 MET cc_start: 0.9626 (mmm) cc_final: 0.9349 (mmm) REVERT: C 483 ASP cc_start: 0.8435 (p0) cc_final: 0.8131 (p0) REVERT: C 512 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8303 (mtt180) REVERT: C 756 ILE cc_start: 0.4008 (OUTLIER) cc_final: 0.3670 (mt) REVERT: D 160 MET cc_start: 0.1439 (mmp) cc_final: 0.0709 (ppp) REVERT: D 354 VAL cc_start: 0.8834 (m) cc_final: 0.8620 (t) REVERT: D 713 MET cc_start: 0.8759 (tpp) cc_final: 0.8403 (tpp) REVERT: E 160 MET cc_start: 0.7628 (mmp) cc_final: 0.7132 (tpp) REVERT: E 256 VAL cc_start: 0.4419 (OUTLIER) cc_final: 0.4004 (t) REVERT: E 276 MET cc_start: 0.4682 (mmp) cc_final: 0.4431 (mmm) REVERT: E 404 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6728 (mmmt) REVERT: E 409 MET cc_start: 0.8909 (tpp) cc_final: 0.8612 (tpt) REVERT: E 657 PHE cc_start: 0.8902 (t80) cc_final: 0.8549 (t80) outliers start: 84 outliers final: 44 residues processed: 239 average time/residue: 0.3818 time to fit residues: 152.3594 Evaluate side-chains 212 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 330 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 365 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 234 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 278 GLN E 310 HIS ** E 666 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 = 0.4348 r_free = 0.4348 target = 0.098429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.071346 restraints weight = 283171.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.069310 restraints weight = 224003.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.070002 restraints weight = 171855.031| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31031 Z= 0.151 Angle : 0.755 14.545 42075 Z= 0.370 Chirality : 0.046 0.414 4786 Planarity : 0.005 0.058 5464 Dihedral : 7.357 134.917 4299 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.76 % Allowed : 16.02 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3855 helix: -0.16 (0.13), residues: 1665 sheet: -2.04 (0.26), residues: 382 loop : -2.07 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 298 HIS 0.007 0.001 HIS B 407 PHE 0.012 0.001 PHE E 466 TYR 0.019 0.002 TYR A 225 ARG 0.010 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 1287) hydrogen bonds : angle 5.51557 ( 3756) covalent geometry : bond 0.00327 (31031) covalent geometry : angle 0.75541 (42075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4305 (tpt) cc_final: 0.3638 (tpt) REVERT: A 496 MET cc_start: 0.8556 (mmp) cc_final: 0.8164 (mmp) REVERT: A 698 MET cc_start: 0.3728 (mtt) cc_final: 0.3254 (mtt) REVERT: B 230 MET cc_start: 0.8290 (ptt) cc_final: 0.7872 (ppp) REVERT: B 439 MET cc_start: 0.7915 (tmm) cc_final: 0.7590 (ppp) REVERT: B 472 ASN cc_start: 0.8695 (t0) cc_final: 0.8235 (p0) REVERT: B 600 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6083 (pp) REVERT: C 143 ARG cc_start: 0.9497 (ttp80) cc_final: 0.9000 (tpm170) REVERT: C 217 MET cc_start: 0.8868 (ppp) cc_final: 0.8655 (pmm) REVERT: C 276 MET cc_start: 0.8354 (tmm) cc_final: 0.8008 (tmm) REVERT: C 439 MET cc_start: 0.9583 (mmm) cc_final: 0.9122 (mmm) REVERT: C 443 LEU cc_start: 0.9576 (mt) cc_final: 0.9327 (mt) REVERT: C 483 ASP cc_start: 0.8430 (p0) cc_final: 0.8226 (p0) REVERT: C 683 MET cc_start: 0.8475 (ptp) cc_final: 0.8181 (ptp) REVERT: D 160 MET cc_start: 0.1473 (mmp) cc_final: 0.0750 (ppp) REVERT: D 317 GLU cc_start: 0.8201 (pp20) cc_final: 0.7861 (pp20) REVERT: D 354 VAL cc_start: 0.8708 (m) cc_final: 0.8455 (t) REVERT: D 437 SER cc_start: 0.9521 (m) cc_final: 0.9238 (p) REVERT: D 499 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (mm-40) REVERT: D 713 MET cc_start: 0.8700 (tpp) cc_final: 0.8402 (tpp) REVERT: E 276 MET cc_start: 0.5381 (mmp) cc_final: 0.4843 (mmm) REVERT: E 409 MET cc_start: 0.8927 (tpp) cc_final: 0.8639 (tpt) REVERT: E 657 PHE cc_start: 0.8965 (t80) cc_final: 0.8536 (t80) outliers start: 57 outliers final: 39 residues processed: 228 average time/residue: 0.4183 time to fit residues: 157.5762 Evaluate side-chains 212 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 256 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 133 optimal weight: 0.0070 chunk 187 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 HIS E 475 GLN ** E 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.082446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.057710 restraints weight = 149072.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.057699 restraints weight = 152264.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.057699 restraints weight = 150673.925| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31031 Z= 0.228 Angle : 0.806 17.093 42075 Z= 0.397 Chirality : 0.047 0.309 4786 Planarity : 0.006 0.061 5464 Dihedral : 7.404 132.788 4299 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.68 % Favored : 90.30 % Rotamer: Outliers : 2.07 % Allowed : 16.33 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3855 helix: -0.19 (0.13), residues: 1665 sheet: -2.21 (0.25), residues: 395 loop : -2.05 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 298 HIS 0.008 0.002 HIS E 454 PHE 0.015 0.002 PHE E 466 TYR 0.026 0.002 TYR D 643 ARG 0.012 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 1287) hydrogen bonds : angle 5.63812 ( 3756) covalent geometry : bond 0.00477 (31031) covalent geometry : angle 0.80617 (42075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8079 (mmp) cc_final: 0.7719 (mmm) REVERT: A 160 MET cc_start: 0.7550 (mmm) cc_final: 0.7261 (mmm) REVERT: A 427 MET cc_start: 0.5165 (tpt) cc_final: 0.4742 (tpt) REVERT: A 496 MET cc_start: 0.8375 (mmp) cc_final: 0.8010 (mmp) REVERT: B 439 MET cc_start: 0.8645 (tmm) cc_final: 0.8176 (ppp) REVERT: B 472 ASN cc_start: 0.9446 (t0) cc_final: 0.9144 (p0) REVERT: B 567 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6967 (mtt-85) REVERT: C 409 MET cc_start: 0.8778 (tpp) cc_final: 0.8417 (tpp) REVERT: C 439 MET cc_start: 0.9785 (mmm) cc_final: 0.9354 (mmm) REVERT: C 443 LEU cc_start: 0.9510 (mt) cc_final: 0.9281 (mt) REVERT: D 160 MET cc_start: 0.1727 (mmp) cc_final: 0.0716 (ppp) REVERT: D 354 VAL cc_start: 0.8616 (m) cc_final: 0.8350 (t) REVERT: D 437 SER cc_start: 0.9556 (m) cc_final: 0.9347 (p) REVERT: D 713 MET cc_start: 0.8820 (tpp) cc_final: 0.8465 (tpp) REVERT: E 256 VAL cc_start: 0.4732 (OUTLIER) cc_final: 0.4290 (t) REVERT: E 276 MET cc_start: 0.5141 (mmp) cc_final: 0.4760 (mmm) REVERT: E 404 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7132 (mmmt) REVERT: E 469 THR cc_start: 0.4826 (OUTLIER) cc_final: 0.4595 (p) REVERT: E 657 PHE cc_start: 0.9067 (t80) cc_final: 0.8639 (t80) outliers start: 67 outliers final: 53 residues processed: 227 average time/residue: 0.4003 time to fit residues: 150.1956 Evaluate side-chains 219 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 179 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 chunk 171 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 454 HIS ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 742 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.095735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.068813 restraints weight = 286549.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068613 restraints weight = 241540.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.067245 restraints weight = 194507.248| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31031 Z= 0.261 Angle : 0.870 14.465 42075 Z= 0.433 Chirality : 0.049 0.375 4786 Planarity : 0.006 0.064 5464 Dihedral : 7.660 131.658 4299 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.07 % Allowed : 17.01 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3855 helix: -0.40 (0.12), residues: 1681 sheet: -2.22 (0.26), residues: 369 loop : -2.14 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 298 HIS 0.010 0.002 HIS E 454 PHE 0.016 0.002 PHE E 466 TYR 0.033 0.002 TYR D 643 ARG 0.011 0.001 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 1287) hydrogen bonds : angle 5.84793 ( 3756) covalent geometry : bond 0.00546 (31031) covalent geometry : angle 0.87013 (42075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 168 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4663 (tpt) cc_final: 0.4438 (tpt) REVERT: A 496 MET cc_start: 0.8510 (mmp) cc_final: 0.8163 (mmp) REVERT: A 698 MET cc_start: 0.3852 (mtt) cc_final: 0.3026 (mtt) REVERT: B 410 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8430 (ttpt) REVERT: B 439 MET cc_start: 0.7956 (tmm) cc_final: 0.7743 (ppp) REVERT: B 472 ASN cc_start: 0.8589 (t0) cc_final: 0.8366 (p0) REVERT: B 567 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6981 (mtt-85) REVERT: C 143 ARG cc_start: 0.9515 (tmm160) cc_final: 0.9107 (tpm170) REVERT: C 276 MET cc_start: 0.8399 (tmm) cc_final: 0.8179 (tmm) REVERT: C 409 MET cc_start: 0.8837 (tpp) cc_final: 0.8488 (tpp) REVERT: C 439 MET cc_start: 0.9524 (mmm) cc_final: 0.9124 (mmm) REVERT: C 443 LEU cc_start: 0.9588 (mt) cc_final: 0.9371 (mt) REVERT: C 683 MET cc_start: 0.8817 (ptp) cc_final: 0.8574 (pmm) REVERT: D 160 MET cc_start: 0.1491 (mmp) cc_final: 0.0752 (ppp) REVERT: D 320 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7419 (t80) REVERT: D 354 VAL cc_start: 0.8687 (m) cc_final: 0.8460 (t) REVERT: D 401 MET cc_start: 0.8693 (ppp) cc_final: 0.8367 (ppp) REVERT: D 437 SER cc_start: 0.9496 (m) cc_final: 0.9205 (p) REVERT: D 584 ARG cc_start: 0.0284 (OUTLIER) cc_final: -0.2878 (ptp90) REVERT: D 698 MET cc_start: 0.5268 (tmm) cc_final: 0.4985 (tmm) REVERT: D 713 MET cc_start: 0.8794 (tpp) cc_final: 0.8478 (tpp) REVERT: E 256 VAL cc_start: 0.4728 (OUTLIER) cc_final: 0.4367 (t) REVERT: E 276 MET cc_start: 0.5310 (mmp) cc_final: 0.4782 (mmm) REVERT: E 404 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6927 (mmmt) REVERT: E 657 PHE cc_start: 0.9054 (t80) cc_final: 0.8651 (t80) outliers start: 67 outliers final: 51 residues processed: 226 average time/residue: 0.3923 time to fit residues: 146.2828 Evaluate side-chains 221 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 150 optimal weight: 7.9990 chunk 216 optimal weight: 0.0970 chunk 119 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 239 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 292 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 454 HIS B 664 HIS B 727 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS E 340 GLN E 666 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.099588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.072473 restraints weight = 279641.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.070869 restraints weight = 223139.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.071122 restraints weight = 182871.682| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31031 Z= 0.133 Angle : 0.793 17.311 42075 Z= 0.383 Chirality : 0.046 0.269 4786 Planarity : 0.005 0.094 5464 Dihedral : 7.092 135.170 4299 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.20 % Allowed : 18.15 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3855 helix: -0.04 (0.13), residues: 1670 sheet: -2.16 (0.26), residues: 377 loop : -1.91 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 507 HIS 0.006 0.001 HIS C 310 PHE 0.011 0.001 PHE E 466 TYR 0.017 0.001 TYR C 643 ARG 0.027 0.001 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 1287) hydrogen bonds : angle 5.30757 ( 3756) covalent geometry : bond 0.00291 (31031) covalent geometry : angle 0.79310 (42075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4953 (tpt) cc_final: 0.4524 (tpt) REVERT: A 496 MET cc_start: 0.8593 (mmp) cc_final: 0.8206 (mmp) REVERT: A 698 MET cc_start: 0.3711 (mtt) cc_final: 0.3024 (mtt) REVERT: B 230 MET cc_start: 0.8324 (ptt) cc_final: 0.7979 (ppp) REVERT: B 472 ASN cc_start: 0.8779 (t0) cc_final: 0.8342 (t0) REVERT: C 143 ARG cc_start: 0.9529 (tmm160) cc_final: 0.9150 (tpm170) REVERT: C 421 LEU cc_start: 0.9387 (mt) cc_final: 0.9148 (mp) REVERT: C 439 MET cc_start: 0.9568 (mmm) cc_final: 0.9096 (mmm) REVERT: C 443 LEU cc_start: 0.9582 (mt) cc_final: 0.9308 (mt) REVERT: C 516 MET cc_start: 0.6988 (tmm) cc_final: 0.6699 (tmm) REVERT: D 160 MET cc_start: 0.1309 (mmp) cc_final: 0.0604 (ppp) REVERT: D 317 GLU cc_start: 0.8025 (pp20) cc_final: 0.7642 (pp20) REVERT: D 354 VAL cc_start: 0.8537 (m) cc_final: 0.8217 (t) REVERT: D 401 MET cc_start: 0.8207 (ppp) cc_final: 0.7825 (ppp) REVERT: D 437 SER cc_start: 0.9421 (m) cc_final: 0.9129 (p) REVERT: D 698 MET cc_start: 0.5458 (tmm) cc_final: 0.5131 (tmm) REVERT: D 713 MET cc_start: 0.8692 (tpp) cc_final: 0.8358 (tpp) REVERT: E 276 MET cc_start: 0.5581 (mmp) cc_final: 0.5044 (mmm) REVERT: E 409 MET cc_start: 0.8806 (tpp) cc_final: 0.8531 (tpt) REVERT: E 469 THR cc_start: 0.4489 (OUTLIER) cc_final: 0.4231 (p) REVERT: E 657 PHE cc_start: 0.8964 (t80) cc_final: 0.8569 (t80) outliers start: 39 outliers final: 28 residues processed: 220 average time/residue: 0.4031 time to fit residues: 145.8735 Evaluate side-chains 201 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 292 TRP Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 44 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 144 optimal weight: 0.0170 chunk 315 optimal weight: 0.3980 chunk 289 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 overall best weight: 2.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.098418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.071792 restraints weight = 281709.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.071357 restraints weight = 235975.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.070807 restraints weight = 193929.630| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31031 Z= 0.148 Angle : 0.777 16.798 42075 Z= 0.375 Chirality : 0.045 0.387 4786 Planarity : 0.005 0.053 5464 Dihedral : 6.964 131.045 4299 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.02 % Allowed : 18.73 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3855 helix: 0.12 (0.13), residues: 1672 sheet: -2.19 (0.25), residues: 389 loop : -1.85 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 298 HIS 0.006 0.001 HIS B 407 PHE 0.015 0.001 PHE E 466 TYR 0.017 0.001 TYR C 332 ARG 0.006 0.000 ARG D 432 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1287) hydrogen bonds : angle 5.26903 ( 3756) covalent geometry : bond 0.00325 (31031) covalent geometry : angle 0.77672 (42075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13824.06 seconds wall clock time: 241 minutes 1.49 seconds (14461.49 seconds total)