Starting phenix.real_space_refine on Tue Aug 26 15:14:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.map" model { file = "/net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgo_63069/08_2025/9lgo_63069.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.071 sd= 0.706 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 1 5.21 5 S 172 5.16 5 C 24308 2.51 5 N 6723 2.21 5 O 7178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38406 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5418 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 37, 'TRANS': 662} Chain breaks: 5 Chain: "J" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1420 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain breaks: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1420 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain breaks: 1 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "G" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1623 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "F" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5228 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 54, 'TRANS': 638} Chain breaks: 4 Chain: "E" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5377 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 39, 'TRANS': 659} Chain breaks: 3 Chain: "D" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5498 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 40, 'TRANS': 669} Chain breaks: 3 Chain: "C" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5132 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 53, 'TRANS': 627} Chain breaks: 6 Chain: "B" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5394 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 38, 'TRANS': 662} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.37, per 1000 atoms: 0.22 Number of scatterers: 38406 At special positions: 0 Unit cell: (150.696, 152.88, 165.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 172 16.00 P 24 15.00 Mg 1 11.99 O 7178 8.00 N 6723 7.00 C 24308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9182 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 35 sheets defined 48.6% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.793A pdb=" N GLN A 64 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.555A pdb=" N LYS A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.608A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'A' and resid 399 through 409 Processing helix chain 'A' and resid 430 through 444 removed outlier: 4.317A pdb=" N ARG A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.036A pdb=" N LEU A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.210A pdb=" N LEU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.715A pdb=" N LEU A 509 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 510 " --> pdb=" O ALA A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 510' Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.625A pdb=" N LYS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.656A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 removed outlier: 3.702A pdb=" N LYS A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 572 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.679A pdb=" N PHE A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 4.165A pdb=" N ALA A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 Processing helix chain 'A' and resid 650 through 657 removed outlier: 3.634A pdb=" N ILE A 654 " --> pdb=" O PRO A 650 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.734A pdb=" N MET A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 removed outlier: 4.002A pdb=" N ASN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 700' Processing helix chain 'A' and resid 704 through 720 removed outlier: 3.847A pdb=" N VAL A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 758 removed outlier: 3.527A pdb=" N GLU A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 779 through 784 removed outlier: 3.551A pdb=" N MET A 783 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 784 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.597A pdb=" N LEU A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.782A pdb=" N VAL A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 844 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 869 removed outlier: 3.508A pdb=" N SER A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 Processing helix chain 'J' and resid 18 through 60 removed outlier: 4.012A pdb=" N LYS J 22 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 128 removed outlier: 3.947A pdb=" N ILE J 119 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 170 removed outlier: 3.692A pdb=" N LEU J 161 " --> pdb=" O ARG J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 175 through 189 removed outlier: 3.866A pdb=" N GLN J 189 " --> pdb=" O MET J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 206 removed outlier: 3.672A pdb=" N LEU J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 61 removed outlier: 3.729A pdb=" N ALA I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 127 Processing helix chain 'I' and resid 141 through 170 removed outlier: 4.210A pdb=" N PHE I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 189 removed outlier: 3.910A pdb=" N GLN I 189 " --> pdb=" O MET I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 208 removed outlier: 3.667A pdb=" N GLY I 208 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 97 removed outlier: 4.210A pdb=" N LEU H 69 " --> pdb=" O GLN H 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 72 " --> pdb=" O PRO H 68 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Proline residue: H 81 - end of helix Processing helix chain 'H' and resid 97 through 116 removed outlier: 3.688A pdb=" N LEU H 101 " --> pdb=" O CYS H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 178 removed outlier: 3.991A pdb=" N ARG H 134 " --> pdb=" O ASP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.752A pdb=" N VAL H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 224 Processing helix chain 'H' and resid 230 through 245 removed outlier: 3.544A pdb=" N GLN H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Proline residue: H 237 - end of helix removed outlier: 3.710A pdb=" N ASP H 241 " --> pdb=" O PRO H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 265 removed outlier: 3.542A pdb=" N ILE H 255 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE H 262 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU H 265 " --> pdb=" O PHE H 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 117 Proline residue: G 81 - end of helix removed outlier: 3.636A pdb=" N GLU G 85 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Proline residue: G 99 - end of helix removed outlier: 4.284A pdb=" N LEU G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 178 removed outlier: 3.915A pdb=" N ARG G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.648A pdb=" N VAL G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 224 Processing helix chain 'G' and resid 230 through 235 Processing helix chain 'G' and resid 235 through 247 removed outlier: 3.613A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER G 244 " --> pdb=" O TRP G 240 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU G 247 " --> pdb=" O ILE G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 264 removed outlier: 5.016A pdb=" N PHE G 261 " --> pdb=" O LEU G 257 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE G 262 " --> pdb=" O ASN G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.862A pdb=" N SER F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 221 removed outlier: 3.916A pdb=" N ARG F 221 " --> pdb=" O LEU F 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 221' Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.596A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 258 removed outlier: 3.804A pdb=" N VAL F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 3.616A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 removed outlier: 4.029A pdb=" N ARG F 290 " --> pdb=" O PHE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.998A pdb=" N SER F 319 " --> pdb=" O ARG F 315 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 356 removed outlier: 4.011A pdb=" N ARG F 355 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG F 356 " --> pdb=" O PRO F 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 356' Processing helix chain 'F' and resid 370 through 385 removed outlier: 3.817A pdb=" N ARG F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 376 " --> pdb=" O LYS F 372 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 381 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 384 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 removed outlier: 3.834A pdb=" N THR F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 418 removed outlier: 3.725A pdb=" N THR F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 416 " --> pdb=" O CYS F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.686A pdb=" N PHE F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.704A pdb=" N GLU F 465 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 466 " --> pdb=" O TRP F 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 462 through 466' Processing helix chain 'F' and resid 469 through 478 Processing helix chain 'F' and resid 481 through 486 Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.517A pdb=" N PHE F 490 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 491 " --> pdb=" O PRO F 487 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET F 493 " --> pdb=" O GLU F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 523 removed outlier: 3.634A pdb=" N THR F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 521 " --> pdb=" O ALA F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 3.866A pdb=" N LEU F 534 " --> pdb=" O SER F 530 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 530 through 535' Processing helix chain 'F' and resid 542 through 554 removed outlier: 3.603A pdb=" N PHE F 550 " --> pdb=" O LEU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 597 removed outlier: 3.581A pdb=" N ASP F 595 " --> pdb=" O LEU F 591 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL F 597 " --> pdb=" O GLU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 666 removed outlier: 3.757A pdb=" N SER F 660 " --> pdb=" O LYS F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 684 removed outlier: 3.806A pdb=" N LEU F 680 " --> pdb=" O SER F 676 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F 683 " --> pdb=" O ASN F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 707 removed outlier: 3.675A pdb=" N LEU F 692 " --> pdb=" O SER F 688 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 693 " --> pdb=" O GLY F 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 704 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 722 removed outlier: 3.916A pdb=" N PHE F 719 " --> pdb=" O LYS F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 742 removed outlier: 3.674A pdb=" N LEU F 737 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 739 " --> pdb=" O LEU F 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.916A pdb=" N ASP E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 168 removed outlier: 3.749A pdb=" N LEU E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 186 removed outlier: 3.571A pdb=" N GLY E 185 " --> pdb=" O THR E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 409 removed outlier: 3.999A pdb=" N ASN E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 437 Processing helix chain 'E' and resid 454 through 459 removed outlier: 4.438A pdb=" N CYS E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.975A pdb=" N LEU E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 removed outlier: 3.791A pdb=" N ARG E 511 " --> pdb=" O ALA E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'E' and resid 549 through 556 Processing helix chain 'E' and resid 561 through 573 removed outlier: 3.543A pdb=" N LYS E 565 " --> pdb=" O GLY E 561 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 573 " --> pdb=" O ASN E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 577 through 583 removed outlier: 3.537A pdb=" N LYS E 581 " --> pdb=" O ARG E 577 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 582 " --> pdb=" O ARG E 578 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN E 583 " --> pdb=" O ILE E 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 577 through 583' Processing helix chain 'E' and resid 587 through 592 removed outlier: 3.602A pdb=" N VAL E 591 " --> pdb=" O PRO E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 removed outlier: 4.209A pdb=" N LEU E 603 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN E 604 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 641 removed outlier: 3.785A pdb=" N LEU E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 638 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 649 Processing helix chain 'E' and resid 650 through 657 removed outlier: 3.980A pdb=" N ILE E 654 " --> pdb=" O PRO E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 685 removed outlier: 3.590A pdb=" N MET E 676 " --> pdb=" O CYS E 672 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 685 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 699 removed outlier: 3.707A pdb=" N MET E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 699 " --> pdb=" O PRO E 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 694 through 699' Processing helix chain 'E' and resid 701 through 719 removed outlier: 3.855A pdb=" N ARG E 707 " --> pdb=" O GLY E 703 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 732 Processing helix chain 'E' and resid 741 through 760 removed outlier: 3.506A pdb=" N ALA E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 784 removed outlier: 3.553A pdb=" N MET E 783 " --> pdb=" O LYS E 780 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 784 " --> pdb=" O ALA E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 810 removed outlier: 3.715A pdb=" N GLU E 804 " --> pdb=" O ALA E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 827 removed outlier: 3.659A pdb=" N LEU E 824 " --> pdb=" O ASP E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 850 removed outlier: 3.752A pdb=" N CYS E 840 " --> pdb=" O ILE E 836 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 844 " --> pdb=" O CYS E 840 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 850 " --> pdb=" O LEU E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 869 removed outlier: 3.645A pdb=" N GLN E 864 " --> pdb=" O ARG E 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.805A pdb=" N GLN D 64 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN D 65 " --> pdb=" O THR D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 358 through 375 removed outlier: 3.502A pdb=" N LYS D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) Proline residue: D 372 - end of helix Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.502A pdb=" N SER D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.643A pdb=" N ALA D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 405 " --> pdb=" O THR D 401 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 440 removed outlier: 4.111A pdb=" N ALA D 433 " --> pdb=" O GLY D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 459 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 483 removed outlier: 3.629A pdb=" N VAL D 474 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 487 removed outlier: 3.578A pdb=" N GLU D 487 " --> pdb=" O ILE D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 525 through 537 Processing helix chain 'D' and resid 545 through 556 Processing helix chain 'D' and resid 560 through 582 removed outlier: 3.668A pdb=" N LYS D 565 " --> pdb=" O GLY D 561 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 572 " --> pdb=" O CYS D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 removed outlier: 4.105A pdb=" N ASN D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP D 608 " --> pdb=" O GLN D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 630 removed outlier: 3.937A pdb=" N ILE D 629 " --> pdb=" O SER D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 644 removed outlier: 3.974A pdb=" N ALA D 642 " --> pdb=" O LYS D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 649 removed outlier: 3.596A pdb=" N HIS D 649 " --> pdb=" O TRP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 657 removed outlier: 4.010A pdb=" N ILE D 654 " --> pdb=" O PRO D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 685 removed outlier: 3.652A pdb=" N MET D 676 " --> pdb=" O CYS D 672 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 700 removed outlier: 3.673A pdb=" N LEU D 697 " --> pdb=" O LYS D 693 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 699 " --> pdb=" O PRO D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 719 removed outlier: 3.989A pdb=" N ARG D 707 " --> pdb=" O GLY D 703 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 758 removed outlier: 3.551A pdb=" N THR D 755 " --> pdb=" O ALA D 751 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 756 " --> pdb=" O GLN D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 812 removed outlier: 3.535A pdb=" N ARG D 803 " --> pdb=" O ALA D 799 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 804 " --> pdb=" O ALA D 800 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS D 811 " --> pdb=" O LYS D 807 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 828 removed outlier: 3.737A pdb=" N LEU D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 826 " --> pdb=" O ASP D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 851 removed outlier: 3.654A pdb=" N VAL D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS D 840 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 869 removed outlier: 3.984A pdb=" N PHE D 862 " --> pdb=" O MET D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 885 removed outlier: 3.575A pdb=" N ARG D 878 " --> pdb=" O PRO D 874 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 879 " --> pdb=" O GLU D 875 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.936A pdb=" N ARG C 24 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.754A pdb=" N VAL C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.830A pdb=" N ASP C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.843A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.641A pdb=" N VAL C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.557A pdb=" N LEU C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 removed outlier: 3.781A pdb=" N GLY C 334 " --> pdb=" O GLY C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.625A pdb=" N LEU C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 355 " --> pdb=" O PRO C 352 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 356 " --> pdb=" O ALA C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 356' Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.775A pdb=" N VAL C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.252A pdb=" N GLU C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 400' Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.577A pdb=" N ALA C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.678A pdb=" N PHE C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.621A pdb=" N GLU C 465 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 466 " --> pdb=" O TRP C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 480 through 486 removed outlier: 3.695A pdb=" N LEU C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.724A pdb=" N PHE C 490 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.741A pdb=" N HIS C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 554 removed outlier: 3.612A pdb=" N ILE C 549 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.547A pdb=" N VAL C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 587 " --> pdb=" O GLN C 583 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.765A pdb=" N VAL C 633 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 630 through 634' Processing helix chain 'C' and resid 635 through 640 removed outlier: 3.896A pdb=" N ARG C 640 " --> pdb=" O ALA C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 667 removed outlier: 3.611A pdb=" N SER C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 667 " --> pdb=" O LYS C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 684 removed outlier: 3.528A pdb=" N LEU C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 708 removed outlier: 3.612A pdb=" N ASN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 723 removed outlier: 3.774A pdb=" N PHE C 719 " --> pdb=" O LYS C 715 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 723 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 745 removed outlier: 3.516A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 745 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.072A pdb=" N GLN B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN B 65 " --> pdb=" O THR B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.892A pdb=" N MET B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 79 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.895A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 168 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.459A pdb=" N GLN B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 4.320A pdb=" N ALA B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 removed outlier: 3.531A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.612A pdb=" N ALA B 475 " --> pdb=" O LYS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.702A pdb=" N ALA B 504 " --> pdb=" O ARG B 501 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 505 " --> pdb=" O PRO B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 505' Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.669A pdb=" N LYS B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.683A pdb=" N LEU B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 4.008A pdb=" N ILE B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 4.606A pdb=" N PHE B 602 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.914A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 650 through 657 removed outlier: 3.780A pdb=" N ILE B 654 " --> pdb=" O PRO B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.650A pdb=" N ALA B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 698 removed outlier: 3.677A pdb=" N MET B 698 " --> pdb=" O GLY B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 694 through 698' Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.681A pdb=" N GLU B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 719 " --> pdb=" O LYS B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 732 Processing helix chain 'B' and resid 739 through 760 removed outlier: 3.994A pdb=" N GLY B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 745 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 778 removed outlier: 3.555A pdb=" N ARG B 777 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 774 through 778' Processing helix chain 'B' and resid 798 through 810 removed outlier: 3.631A pdb=" N ARG B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 827 Processing helix chain 'B' and resid 832 through 851 removed outlier: 3.569A pdb=" N ILE B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 869 removed outlier: 4.031A pdb=" N PHE B 862 " --> pdb=" O MET B 858 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 864 " --> pdb=" O ARG B 860 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49 removed outlier: 8.354A pdb=" N VAL A 111 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR A 47 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 69 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 70 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.758A pdb=" N TYR A 324 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 137 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 325 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 139 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 141 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 197 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 143 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 195 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP A 145 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 181 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.758A pdb=" N TYR A 324 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 137 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 325 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 139 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 148 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 418 removed outlier: 5.993A pdb=" N SER A 416 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP A 453 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 418 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 389 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 692 removed outlier: 6.455A pdb=" N SER A 722 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A 769 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 724 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA A 771 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE A 726 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 664 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR A 772 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 666 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 72 removed outlier: 8.060A pdb=" N VAL F 72 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS F 15 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'F' and resid 28 through 31 removed outlier: 4.741A pdb=" N CYS F 78 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA F 111 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY F 168 " --> pdb=" O ARG F 109 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG F 109 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 143 through 144 Processing sheet with id=AB1, first strand: chain 'F' and resid 261 through 263 removed outlier: 3.733A pdb=" N LEU F 299 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 263 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL F 339 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU F 238 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 525 through 529 removed outlier: 6.392A pdb=" N LEU F 502 " --> pdb=" O ILE F 648 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AB4, first strand: chain 'E' and resid 95 through 99 Processing sheet with id=AB5, first strand: chain 'E' and resid 191 through 197 removed outlier: 4.985A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 145 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 143 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 191 through 197 removed outlier: 4.985A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 145 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 143 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N ARG E 331 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU E 142 " --> pdb=" O ARG E 331 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN E 333 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET E 144 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR E 335 " --> pdb=" O MET E 144 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 146 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 392 through 393 removed outlier: 6.944A pdb=" N LEU E 392 " --> pdb=" O THR E 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 415 through 418 Processing sheet with id=AB9, first strand: chain 'E' and resid 688 through 693 removed outlier: 6.094A pdb=" N ASN E 688 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE E 725 " --> pdb=" O ASN E 688 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 690 " --> pdb=" O PHE E 725 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP E 727 " --> pdb=" O LEU E 690 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE E 692 " --> pdb=" O ASP E 727 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY E 663 " --> pdb=" O ARG E 790 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ILE E 792 " --> pdb=" O GLY E 663 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 665 " --> pdb=" O ILE E 792 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 50 removed outlier: 8.341A pdb=" N VAL D 111 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR D 47 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 113 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 49 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 70 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 172 through 173 removed outlier: 4.860A pdb=" N TYR D 324 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA D 137 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE D 325 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 139 " --> pdb=" O PHE D 325 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 141 " --> pdb=" O GLY D 197 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY D 197 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU D 143 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL D 195 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP D 145 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 172 through 173 removed outlier: 4.860A pdb=" N TYR D 324 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA D 137 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE D 325 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 139 " --> pdb=" O PHE D 325 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ARG D 331 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU D 142 " --> pdb=" O ARG D 331 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASN D 333 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET D 144 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 335 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL D 146 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 415 through 418 removed outlier: 4.200A pdb=" N LEU D 494 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 450 " --> pdb=" O LEU D 494 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 496 " --> pdb=" O ILE D 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 688 through 692 removed outlier: 6.500A pdb=" N ASN D 688 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 725 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 690 " --> pdb=" O PHE D 725 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 664 " --> pdb=" O ILE D 768 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY D 663 " --> pdb=" O ILE D 788 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 790 " --> pdb=" O GLY D 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 71 through 72 removed outlier: 7.965A pdb=" N VAL C 72 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS C 15 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AC8, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.698A pdb=" N CYS C 78 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 111 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 168 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG C 109 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 110 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 262 through 265 removed outlier: 6.324A pdb=" N LEU C 300 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA C 343 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 302 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 237 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR C 344 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 239 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 236 " --> pdb=" O ARG C 362 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 364 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C 238 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 525 through 529 removed outlier: 7.263A pdb=" N ALA C 559 " --> pdb=" O MET C 623 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE C 625 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 561 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA C 627 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C 563 " --> pdb=" O ALA C 627 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 504 " --> pdb=" O ILE C 648 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AD3, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AD4, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.831A pdb=" N LEU B 139 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR B 324 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.620A pdb=" N LEU B 179 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 190 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 181 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.620A pdb=" N LEU B 179 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 190 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 181 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 145 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL B 195 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 143 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 415 through 419 removed outlier: 4.170A pdb=" N PHE B 451 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 418 " --> pdb=" O PHE B 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 688 through 693 removed outlier: 6.864A pdb=" N GLY B 663 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG B 790 " --> pdb=" O GLY B 663 " (cutoff:3.500A) 1567 hydrogen bonds defined for protein. 4614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8959 1.33 - 1.45: 7462 1.45 - 1.58: 22338 1.58 - 1.70: 34 1.70 - 1.82: 272 Bond restraints: 39065 Sorted by residual: bond pdb=" C ARG H 67 " pdb=" N PRO H 68 " ideal model delta sigma weight residual 1.335 1.434 -0.098 1.36e-02 5.41e+03 5.23e+01 bond pdb=" CA LYS F 744 " pdb=" C LYS F 744 " ideal model delta sigma weight residual 1.529 1.475 0.054 9.30e-03 1.16e+04 3.39e+01 bond pdb=" CA ASP D 56 " pdb=" C ASP D 56 " ideal model delta sigma weight residual 1.524 1.474 0.050 8.80e-03 1.29e+04 3.21e+01 bond pdb=" CA LEU F 741 " pdb=" C LEU F 741 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.29e-02 6.01e+03 2.92e+01 bond pdb=" CA ARG A 501 " pdb=" C ARG A 501 " ideal model delta sigma weight residual 1.524 1.456 0.067 1.26e-02 6.30e+03 2.85e+01 ... (remaining 39060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 50929 2.94 - 5.88: 1637 5.88 - 8.81: 299 8.81 - 11.75: 86 11.75 - 14.69: 7 Bond angle restraints: 52958 Sorted by residual: angle pdb=" N ASN E 554 " pdb=" CA ASN E 554 " pdb=" C ASN E 554 " ideal model delta sigma weight residual 111.07 97.89 13.18 1.07e+00 8.73e-01 1.52e+02 angle pdb=" N GLN E 534 " pdb=" CA GLN E 534 " pdb=" C GLN E 534 " ideal model delta sigma weight residual 111.03 97.72 13.31 1.11e+00 8.12e-01 1.44e+02 angle pdb=" C ILE F 453 " pdb=" N GLY F 454 " pdb=" CA GLY F 454 " ideal model delta sigma weight residual 122.33 113.82 8.51 7.30e-01 1.88e+00 1.36e+02 angle pdb=" N ASP F 674 " pdb=" CA ASP F 674 " pdb=" C ASP F 674 " ideal model delta sigma weight residual 114.75 101.11 13.64 1.26e+00 6.30e-01 1.17e+02 angle pdb=" N PRO F 652 " pdb=" CA PRO F 652 " pdb=" C PRO F 652 " ideal model delta sigma weight residual 110.58 100.35 10.23 1.07e+00 8.73e-01 9.15e+01 ... (remaining 52953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 21430 17.87 - 35.74: 2211 35.74 - 53.62: 455 53.62 - 71.49: 95 71.49 - 89.36: 31 Dihedral angle restraints: 24222 sinusoidal: 10045 harmonic: 14177 Sorted by residual: dihedral pdb=" CA SER D 66 " pdb=" C SER D 66 " pdb=" N LEU D 67 " pdb=" CA LEU D 67 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY D 420 " pdb=" C GLY D 420 " pdb=" N PRO D 421 " pdb=" CA PRO D 421 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA THR E 870 " pdb=" C THR E 870 " pdb=" N PRO E 871 " pdb=" CA PRO E 871 " ideal model delta harmonic sigma weight residual 180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 24219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5171 0.084 - 0.168: 865 0.168 - 0.252: 103 0.252 - 0.337: 13 0.337 - 0.421: 2 Chirality restraints: 6154 Sorted by residual: chirality pdb=" CB ILE E 423 " pdb=" CA ILE E 423 " pdb=" CG1 ILE E 423 " pdb=" CG2 ILE E 423 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE D 873 " pdb=" CA ILE D 873 " pdb=" CG1 ILE D 873 " pdb=" CG2 ILE D 873 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CG LEU F 420 " pdb=" CB LEU F 420 " pdb=" CD1 LEU F 420 " pdb=" CD2 LEU F 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 6151 not shown) Planarity restraints: 6811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 608 " -0.026 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C ASP D 608 " 0.088 2.00e-02 2.50e+03 pdb=" O ASP D 608 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE D 609 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 395 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO E 396 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 99 " 0.023 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C THR D 99 " -0.077 2.00e-02 2.50e+03 pdb=" O THR D 99 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA D 100 " 0.026 2.00e-02 2.50e+03 ... (remaining 6808 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 614 2.65 - 3.21: 31430 3.21 - 3.77: 55113 3.77 - 4.34: 72569 4.34 - 4.90: 118254 Nonbonded interactions: 277980 Sorted by model distance: nonbonded pdb=" NZ LYS C 744 " pdb=" CB GLU C 745 " model vdw 2.083 3.520 nonbonded pdb=" OG1 THR C 248 " pdb="MG MG C 803 " model vdw 2.147 2.170 nonbonded pdb=" O MET D 153 " pdb=" N ILE D 155 " model vdw 2.212 3.120 nonbonded pdb=" O LEU J 112 " pdb=" OG1 THR J 115 " model vdw 2.247 3.040 nonbonded pdb=" O SER F 556 " pdb=" OG1 THR F 557 " model vdw 2.265 3.040 ... (remaining 277975 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 44 through 336 or resid 350 through 612 or resid 623 throu \ gh 732 or resid 744 through 871 or resid 901)) selection = (chain 'B' and (resid 44 through 204 or resid 316 through 336 or resid 350 throu \ gh 446 or resid 448 through 581 or resid 595 through 612 or resid 623 through 73 \ 2 or resid 744 through 901)) selection = (chain 'D' and (resid 44 through 336 or resid 350 through 446 or resid 448 throu \ gh 581 or resid 595 through 612 or resid 623 through 871 or resid 901)) selection = (chain 'E' and (resid 44 through 204 or resid 316 through 336 or resid 350 throu \ gh 446 or resid 448 through 581 or resid 595 through 612 or resid 623 through 73 \ 2 or resid 744 through 901)) } ncs_group { reference = (chain 'C' and (resid 12 through 118 or resid 127 through 572 or resid 581 throu \ gh 802)) selection = (chain 'F' and (resid 12 through 191 or resid 200 through 308 or resid 319 throu \ gh 537 or resid 540 through 596 or resid 620 through 802)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 66 through 265) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.560 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.098 39065 Z= 0.474 Angle : 1.262 14.690 52958 Z= 0.707 Chirality : 0.063 0.421 6154 Planarity : 0.010 0.116 6811 Dihedral : 15.202 89.362 15040 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.39 % Favored : 90.71 % Rotamer: Outliers : 2.12 % Allowed : 2.05 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.10), residues: 4863 helix: -3.51 (0.07), residues: 2112 sheet: -0.09 (0.21), residues: 655 loop : -2.63 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 126 TYR 0.045 0.003 TYR J 146 PHE 0.060 0.003 PHE E 806 TRP 0.032 0.003 TRP B 101 HIS 0.013 0.002 HIS A 811 Details of bonding type rmsd covalent geometry : bond 0.00807 (39065) covalent geometry : angle 1.26177 (52958) hydrogen bonds : bond 0.27843 ( 1554) hydrogen bonds : angle 8.46241 ( 4614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 566 time to evaluate : 1.387 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 158 GLU cc_start: 0.7547 (pp20) cc_final: 0.7311 (pp20) REVERT: A 366 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: A 434 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8065 (ttmm) REVERT: A 851 ASP cc_start: 0.8127 (t0) cc_final: 0.7902 (t0) REVERT: J 106 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8379 (tp40) REVERT: I 29 ASP cc_start: 0.7650 (m-30) cc_final: 0.7442 (m-30) REVERT: I 121 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8122 (mt-10) REVERT: F 108 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7961 (mtm110) REVERT: F 205 LEU cc_start: 0.9070 (mt) cc_final: 0.8612 (mt) REVERT: F 221 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.6924 (ttp80) REVERT: F 403 TYR cc_start: 0.8176 (m-80) cc_final: 0.7931 (m-10) REVERT: F 445 GLN cc_start: 0.8107 (pp30) cc_final: 0.7816 (pp30) REVERT: E 143 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7250 (mt-10) REVERT: E 577 ARG cc_start: 0.7586 (mtm180) cc_final: 0.7348 (mtp180) REVERT: E 578 ARG cc_start: 0.8389 (ptp90) cc_final: 0.7800 (ptp90) REVERT: D 56 ASP cc_start: 0.8348 (t0) cc_final: 0.8097 (t0) REVERT: D 110 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8518 (mttp) REVERT: D 480 LEU cc_start: 0.7957 (tp) cc_final: 0.7710 (tp) REVERT: D 614 MET cc_start: 0.8537 (ttp) cc_final: 0.8254 (ttm) REVERT: C 281 ASN cc_start: 0.8330 (m110) cc_final: 0.7961 (m110) REVERT: B 72 LEU cc_start: 0.8294 (mm) cc_final: 0.8038 (mp) REVERT: B 98 TYR cc_start: 0.7874 (m-80) cc_final: 0.7667 (m-80) REVERT: B 142 GLU cc_start: 0.8399 (mp0) cc_final: 0.7981 (mp0) REVERT: B 481 MET cc_start: 0.7429 (ptm) cc_final: 0.7137 (ptm) REVERT: B 530 LEU cc_start: 0.7178 (mm) cc_final: 0.6657 (mm) REVERT: B 578 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6733 (mtt-85) REVERT: B 870 THR cc_start: 0.7856 (t) cc_final: 0.7593 (p) outliers start: 88 outliers final: 48 residues processed: 622 average time/residue: 0.2504 time to fit residues: 236.4157 Evaluate side-chains 535 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 486 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain J residue 120 CYS Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 206 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 213 ARG Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 450 ARG Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 535 LYS Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain E residue 736 ARG Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS A 527 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 752 GLN A 827 GLN J 26 ASN J 126 HIS J 138 HIS I 138 HIS F 311 GLN F 552 GLN F 583 GLN F 679 ASN F 716 GLN E 140 GLN ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN D 500 ASN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.082268 restraints weight = 98033.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084121 restraints weight = 52819.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085604 restraints weight = 37237.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086069 restraints weight = 28684.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086785 restraints weight = 25749.162| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 39065 Z= 0.169 Angle : 0.697 11.358 52958 Z= 0.359 Chirality : 0.045 0.233 6154 Planarity : 0.006 0.070 6811 Dihedral : 10.236 85.557 5703 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 1.71 % Allowed : 8.53 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.11), residues: 4863 helix: -1.11 (0.10), residues: 2165 sheet: 0.37 (0.21), residues: 632 loop : -2.13 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 331 TYR 0.026 0.002 TYR C 222 PHE 0.021 0.002 PHE E 806 TRP 0.021 0.001 TRP G 90 HIS 0.009 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00374 (39065) covalent geometry : angle 0.69700 (52958) hydrogen bonds : bond 0.07610 ( 1554) hydrogen bonds : angle 5.08361 ( 4614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 517 time to evaluate : 0.970 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 366 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7828 (mmm-85) REVERT: A 445 ARG cc_start: 0.7340 (mpp-170) cc_final: 0.7055 (mpp-170) REVERT: A 501 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (ptp-170) REVERT: J 24 LYS cc_start: 0.8881 (pttm) cc_final: 0.8540 (ptpp) REVERT: I 29 ASP cc_start: 0.7856 (m-30) cc_final: 0.7618 (m-30) REVERT: F 108 ARG cc_start: 0.8141 (mpp80) cc_final: 0.7804 (mtm180) REVERT: F 109 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7507 (mtm-85) REVERT: F 403 TYR cc_start: 0.8397 (m-80) cc_final: 0.7974 (m-10) REVERT: F 417 MET cc_start: 0.8868 (tpp) cc_final: 0.8484 (tpt) REVERT: F 445 GLN cc_start: 0.8100 (pp30) cc_final: 0.7727 (pp30) REVERT: F 456 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6954 (mpt) REVERT: F 543 GLU cc_start: 0.7305 (mp0) cc_final: 0.7097 (mp0) REVERT: F 747 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5278 (m-80) REVERT: E 735 GLU cc_start: 0.6779 (pp20) cc_final: 0.6573 (pp20) REVERT: D 56 ASP cc_start: 0.7983 (t0) cc_final: 0.7672 (t0) REVERT: D 67 LEU cc_start: 0.9189 (tp) cc_final: 0.8966 (tp) REVERT: D 110 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8428 (mttp) REVERT: D 150 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7654 (p0) REVERT: D 152 ASP cc_start: 0.7270 (t70) cc_final: 0.6906 (t70) REVERT: C 543 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: C 585 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7223 (ttp80) REVERT: C 742 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: B 436 ARG cc_start: 0.8620 (mmp80) cc_final: 0.8153 (mmp80) REVERT: B 481 MET cc_start: 0.7095 (ptm) cc_final: 0.6860 (ptm) outliers start: 71 outliers final: 39 residues processed: 559 average time/residue: 0.2492 time to fit residues: 211.2650 Evaluate side-chains 523 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 478 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 544 LYS Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 161 optimal weight: 9.9990 chunk 312 optimal weight: 6.9990 chunk 129 optimal weight: 0.0570 chunk 78 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 462 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN I 188 HIS F 583 GLN E 437 GLN D 79 ASN D 140 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082195 restraints weight = 98051.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083811 restraints weight = 55478.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.084339 restraints weight = 39716.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.084607 restraints weight = 36092.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.084728 restraints weight = 34144.841| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39065 Z= 0.153 Angle : 0.643 10.708 52958 Z= 0.327 Chirality : 0.044 0.179 6154 Planarity : 0.005 0.064 6811 Dihedral : 9.311 86.664 5633 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.89 % Rotamer: Outliers : 1.83 % Allowed : 11.23 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.12), residues: 4863 helix: -0.02 (0.11), residues: 2203 sheet: 0.41 (0.21), residues: 647 loop : -1.87 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.015 0.001 TYR C 222 PHE 0.020 0.001 PHE C 441 TRP 0.020 0.001 TRP G 90 HIS 0.006 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00340 (39065) covalent geometry : angle 0.64314 (52958) hydrogen bonds : bond 0.06882 ( 1554) hydrogen bonds : angle 4.64853 ( 4614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 506 time to evaluate : 1.261 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 57 ASP cc_start: 0.8380 (t0) cc_final: 0.7916 (t0) REVERT: A 158 GLU cc_start: 0.7775 (pp20) cc_final: 0.7464 (pp20) REVERT: A 501 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7959 (ptp-170) REVERT: J 24 LYS cc_start: 0.8868 (pttm) cc_final: 0.8654 (pttp) REVERT: J 111 LYS cc_start: 0.8709 (tppp) cc_final: 0.8488 (tppp) REVERT: I 29 ASP cc_start: 0.7858 (m-30) cc_final: 0.7599 (m-30) REVERT: F 108 ARG cc_start: 0.8110 (mpp80) cc_final: 0.7890 (mtm110) REVERT: F 221 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.6999 (ttp80) REVERT: F 372 LYS cc_start: 0.8770 (tptt) cc_final: 0.8551 (tptp) REVERT: F 403 TYR cc_start: 0.8312 (m-80) cc_final: 0.7967 (m-10) REVERT: F 417 MET cc_start: 0.8901 (tpp) cc_final: 0.8548 (tpt) REVERT: F 445 GLN cc_start: 0.8132 (pp30) cc_final: 0.7770 (pp30) REVERT: F 543 GLU cc_start: 0.7338 (mp0) cc_final: 0.6806 (mp0) REVERT: F 620 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6666 (mmm160) REVERT: E 201 MET cc_start: 0.6531 (mtm) cc_final: 0.6227 (mtm) REVERT: D 67 LEU cc_start: 0.9213 (tp) cc_final: 0.8988 (tp) REVERT: C 280 GLU cc_start: 0.8337 (tp30) cc_final: 0.8076 (tp30) REVERT: C 281 ASN cc_start: 0.8282 (m110) cc_final: 0.8053 (m-40) REVERT: C 284 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7836 (mtm-85) REVERT: C 304 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 543 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: C 585 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7216 (ttp80) REVERT: C 742 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: B 75 MET cc_start: 0.7443 (ppp) cc_final: 0.6931 (pmm) REVERT: B 324 TYR cc_start: 0.6789 (m-80) cc_final: 0.5652 (m-10) REVERT: B 354 MET cc_start: 0.8944 (ppp) cc_final: 0.8564 (ppp) REVERT: B 436 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8261 (mmp80) REVERT: B 481 MET cc_start: 0.7151 (ptm) cc_final: 0.6888 (ptm) outliers start: 76 outliers final: 45 residues processed: 546 average time/residue: 0.2322 time to fit residues: 193.8519 Evaluate side-chains 531 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 483 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 120 CYS Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 198 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 466 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 413 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 406 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN F 324 GLN E 361 GLN C 373 GLN B 534 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.077749 restraints weight = 99694.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.079713 restraints weight = 52582.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.081121 restraints weight = 36425.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081930 restraints weight = 28257.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.082489 restraints weight = 24440.543| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39065 Z= 0.190 Angle : 0.671 13.626 52958 Z= 0.338 Chirality : 0.045 0.226 6154 Planarity : 0.005 0.057 6811 Dihedral : 9.132 88.753 5624 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.16 % Favored : 92.74 % Rotamer: Outliers : 1.90 % Allowed : 13.04 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.12), residues: 4863 helix: 0.41 (0.11), residues: 2203 sheet: 0.50 (0.21), residues: 640 loop : -1.75 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 539 TYR 0.015 0.002 TYR A 393 PHE 0.016 0.002 PHE D 451 TRP 0.020 0.002 TRP G 90 HIS 0.008 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00440 (39065) covalent geometry : angle 0.67075 (52958) hydrogen bonds : bond 0.07314 ( 1554) hydrogen bonds : angle 4.61868 ( 4614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 506 time to evaluate : 1.347 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 57 ASP cc_start: 0.8471 (t0) cc_final: 0.8002 (t0) REVERT: A 501 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8175 (ptp-170) REVERT: J 24 LYS cc_start: 0.8879 (pttm) cc_final: 0.8653 (pttp) REVERT: J 111 LYS cc_start: 0.8729 (tppp) cc_final: 0.8485 (tppp) REVERT: I 29 ASP cc_start: 0.7996 (m-30) cc_final: 0.7676 (m-30) REVERT: G 123 PRO cc_start: 0.7384 (Cg_exo) cc_final: 0.7100 (Cg_endo) REVERT: F 221 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7167 (ttp80) REVERT: F 372 LYS cc_start: 0.8898 (tptt) cc_final: 0.8570 (tmtt) REVERT: F 403 TYR cc_start: 0.8445 (m-10) cc_final: 0.8112 (m-10) REVERT: F 417 MET cc_start: 0.8724 (tpp) cc_final: 0.8333 (tpt) REVERT: F 543 GLU cc_start: 0.7484 (mp0) cc_final: 0.6901 (mp0) REVERT: F 620 ARG cc_start: 0.6942 (mmm160) cc_final: 0.6720 (mmm160) REVERT: E 75 MET cc_start: 0.7830 (tpt) cc_final: 0.7458 (tpt) REVERT: E 201 MET cc_start: 0.6502 (mtm) cc_final: 0.6222 (mtm) REVERT: E 735 GLU cc_start: 0.6913 (pp20) cc_final: 0.6449 (pp20) REVERT: D 494 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 284 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: C 304 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 742 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 75 MET cc_start: 0.7452 (ppp) cc_final: 0.7144 (pmm) REVERT: B 351 THR cc_start: 0.8071 (p) cc_final: 0.7858 (p) REVERT: B 354 MET cc_start: 0.8890 (ppp) cc_final: 0.8664 (pmm) REVERT: B 436 ARG cc_start: 0.8724 (mmp80) cc_final: 0.8320 (mmp80) REVERT: B 481 MET cc_start: 0.7162 (ptm) cc_final: 0.6884 (ptm) outliers start: 79 outliers final: 52 residues processed: 547 average time/residue: 0.2477 time to fit residues: 206.0205 Evaluate side-chains 541 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 486 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 349 optimal weight: 0.4980 chunk 352 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 409 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 454 GLN E 361 GLN ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.076039 restraints weight = 99269.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.077930 restraints weight = 52869.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.079361 restraints weight = 36855.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.079650 restraints weight = 28942.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.079991 restraints weight = 26363.112| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 39065 Z= 0.230 Angle : 0.710 13.302 52958 Z= 0.360 Chirality : 0.047 0.194 6154 Planarity : 0.005 0.056 6811 Dihedral : 9.108 89.969 5621 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 2.24 % Allowed : 14.97 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.12), residues: 4863 helix: 0.50 (0.11), residues: 2217 sheet: 0.55 (0.21), residues: 606 loop : -1.66 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 585 TYR 0.023 0.002 TYR B 324 PHE 0.022 0.002 PHE F 360 TRP 0.022 0.002 TRP H 90 HIS 0.009 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00543 (39065) covalent geometry : angle 0.70953 (52958) hydrogen bonds : bond 0.07956 ( 1554) hydrogen bonds : angle 4.67390 ( 4614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 498 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8504 (t0) cc_final: 0.8027 (t0) REVERT: A 501 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8114 (ptp-170) REVERT: A 811 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (t-170) REVERT: J 111 LYS cc_start: 0.8793 (tppp) cc_final: 0.8554 (tppp) REVERT: J 117 LYS cc_start: 0.9014 (tppt) cc_final: 0.8724 (tppt) REVERT: I 29 ASP cc_start: 0.7929 (m-30) cc_final: 0.7625 (m-30) REVERT: F 109 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7446 (mtm-85) REVERT: F 221 ARG cc_start: 0.8015 (ptm-80) cc_final: 0.7330 (ttp80) REVERT: F 372 LYS cc_start: 0.8909 (tptt) cc_final: 0.8605 (tmtt) REVERT: F 403 TYR cc_start: 0.8492 (m-10) cc_final: 0.8154 (m-10) REVERT: F 543 GLU cc_start: 0.7597 (mp0) cc_final: 0.7016 (mp0) REVERT: E 75 MET cc_start: 0.8172 (tpt) cc_final: 0.7776 (tpt) REVERT: E 98 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: E 186 ARG cc_start: 0.8338 (tmm160) cc_final: 0.7838 (tmm-80) REVERT: E 201 MET cc_start: 0.6678 (mtm) cc_final: 0.6379 (mtm) REVERT: E 393 TYR cc_start: 0.7085 (m-80) cc_final: 0.6436 (m-80) REVERT: E 735 GLU cc_start: 0.6949 (pp20) cc_final: 0.6428 (pp20) REVERT: D 494 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 284 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: C 290 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8056 (tpp80) REVERT: C 304 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: C 742 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: B 75 MET cc_start: 0.7479 (ppp) cc_final: 0.7261 (pmm) REVERT: B 331 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8114 (mtm-85) REVERT: B 481 MET cc_start: 0.7072 (ptm) cc_final: 0.6804 (ptm) REVERT: B 707 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7811 (mmm160) outliers start: 93 outliers final: 63 residues processed: 553 average time/residue: 0.2672 time to fit residues: 224.4550 Evaluate side-chains 553 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 581 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 59 optimal weight: 0.0970 chunk 330 optimal weight: 0.9990 chunk 451 optimal weight: 0.3980 chunk 185 optimal weight: 3.9990 chunk 472 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.078858 restraints weight = 99615.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.080821 restraints weight = 51978.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.082290 restraints weight = 36064.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083022 restraints weight = 27718.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083022 restraints weight = 24231.842| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39065 Z= 0.134 Angle : 0.631 15.241 52958 Z= 0.315 Chirality : 0.043 0.183 6154 Planarity : 0.005 0.072 6811 Dihedral : 8.589 87.300 5618 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.05 % Rotamer: Outliers : 1.83 % Allowed : 16.20 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 4863 helix: 0.92 (0.11), residues: 2222 sheet: 0.64 (0.21), residues: 609 loop : -1.56 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 538 TYR 0.018 0.001 TYR B 324 PHE 0.019 0.001 PHE D 451 TRP 0.019 0.001 TRP G 90 HIS 0.004 0.001 HIS F 655 Details of bonding type rmsd covalent geometry : bond 0.00289 (39065) covalent geometry : angle 0.63076 (52958) hydrogen bonds : bond 0.06269 ( 1554) hydrogen bonds : angle 4.38258 ( 4614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 491 time to evaluate : 1.508 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 57 ASP cc_start: 0.8424 (t0) cc_final: 0.7996 (t0) REVERT: A 501 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8097 (ptp-170) REVERT: A 811 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (t-170) REVERT: J 24 LYS cc_start: 0.8556 (pttp) cc_final: 0.8275 (ptpp) REVERT: J 111 LYS cc_start: 0.8781 (tppp) cc_final: 0.8552 (tppp) REVERT: I 29 ASP cc_start: 0.8023 (m-30) cc_final: 0.7700 (m-30) REVERT: G 170 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7922 (tmt-80) REVERT: F 217 ARG cc_start: 0.8254 (tmm-80) cc_final: 0.7991 (tmm-80) REVERT: F 221 ARG cc_start: 0.7930 (ptm-80) cc_final: 0.7175 (ttp80) REVERT: F 372 LYS cc_start: 0.8901 (tptt) cc_final: 0.8576 (tmtt) REVERT: F 403 TYR cc_start: 0.8416 (m-10) cc_final: 0.8050 (m-10) REVERT: F 417 MET cc_start: 0.8778 (tpp) cc_final: 0.8406 (tpt) REVERT: F 543 GLU cc_start: 0.7496 (mp0) cc_final: 0.6913 (mp0) REVERT: F 620 ARG cc_start: 0.7127 (mmm160) cc_final: 0.6734 (mmm160) REVERT: E 75 MET cc_start: 0.8221 (tpt) cc_final: 0.7811 (tpt) REVERT: E 201 MET cc_start: 0.6529 (mtm) cc_final: 0.6258 (mtm) REVERT: E 735 GLU cc_start: 0.6917 (pp20) cc_final: 0.6425 (pp20) REVERT: C 181 ARG cc_start: 0.8127 (ptp90) cc_final: 0.7891 (ptp90) REVERT: C 284 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: C 290 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8003 (tpp80) REVERT: C 304 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: C 742 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: B 75 MET cc_start: 0.7434 (ppp) cc_final: 0.6701 (mpp) REVERT: B 331 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8077 (mtm-85) REVERT: B 436 ARG cc_start: 0.8693 (mmp80) cc_final: 0.7988 (mmp80) REVERT: B 481 MET cc_start: 0.7088 (ptm) cc_final: 0.6828 (ptm) REVERT: B 707 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7759 (mmm160) outliers start: 76 outliers final: 48 residues processed: 540 average time/residue: 0.2514 time to fit residues: 207.0619 Evaluate side-chains 522 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 470 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 453 optimal weight: 50.0000 chunk 333 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 380 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 233 optimal weight: 20.0000 chunk 472 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 434 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 GLN ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.076088 restraints weight = 99113.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.078093 restraints weight = 52745.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.079542 restraints weight = 36835.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.080091 restraints weight = 28687.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.080799 restraints weight = 25362.415| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39065 Z= 0.205 Angle : 0.701 15.289 52958 Z= 0.351 Chirality : 0.046 0.301 6154 Planarity : 0.005 0.066 6811 Dihedral : 8.676 89.307 5618 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.46 % Favored : 92.43 % Rotamer: Outliers : 2.29 % Allowed : 16.97 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.12), residues: 4863 helix: 0.84 (0.11), residues: 2228 sheet: 0.70 (0.21), residues: 600 loop : -1.61 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 359 TYR 0.017 0.002 TYR A 393 PHE 0.022 0.002 PHE D 451 TRP 0.019 0.002 TRP G 90 HIS 0.008 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00484 (39065) covalent geometry : angle 0.70147 (52958) hydrogen bonds : bond 0.07462 ( 1554) hydrogen bonds : angle 4.50558 ( 4614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 492 time to evaluate : 1.551 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 57 ASP cc_start: 0.8493 (t0) cc_final: 0.8055 (t0) REVERT: A 153 MET cc_start: 0.8685 (ptm) cc_final: 0.8359 (ppp) REVERT: A 501 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8108 (ptp-170) REVERT: A 777 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6895 (mtm-85) REVERT: A 811 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (t-170) REVERT: J 24 LYS cc_start: 0.8638 (pttp) cc_final: 0.8362 (ptpp) REVERT: J 111 LYS cc_start: 0.8764 (tppp) cc_final: 0.8542 (tppp) REVERT: J 117 LYS cc_start: 0.9016 (tppt) cc_final: 0.8306 (tppt) REVERT: J 146 TYR cc_start: 0.8579 (t80) cc_final: 0.8056 (t80) REVERT: H 216 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (mp) REVERT: F 217 ARG cc_start: 0.8282 (tmm-80) cc_final: 0.8030 (tmm-80) REVERT: F 221 ARG cc_start: 0.8067 (ptm-80) cc_final: 0.7392 (ttp80) REVERT: F 372 LYS cc_start: 0.8967 (tptt) cc_final: 0.8686 (tmtt) REVERT: F 403 TYR cc_start: 0.8427 (m-10) cc_final: 0.8118 (m-10) REVERT: F 543 GLU cc_start: 0.7523 (mp0) cc_final: 0.6854 (mp0) REVERT: E 75 MET cc_start: 0.8186 (tpt) cc_final: 0.7790 (tpt) REVERT: E 201 MET cc_start: 0.6474 (mtm) cc_final: 0.6250 (mtm) REVERT: E 393 TYR cc_start: 0.6984 (m-80) cc_final: 0.6407 (m-80) REVERT: E 735 GLU cc_start: 0.6934 (pp20) cc_final: 0.6518 (pp20) REVERT: C 284 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: C 290 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8050 (tpp80) REVERT: C 304 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 372 LYS cc_start: 0.8501 (tptp) cc_final: 0.8146 (tptp) REVERT: C 373 GLN cc_start: 0.6724 (pm20) cc_final: 0.6523 (pm20) REVERT: C 544 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8395 (mmmt) REVERT: C 742 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 75 MET cc_start: 0.7393 (ppp) cc_final: 0.6701 (mpp) REVERT: B 361 GLN cc_start: 0.7858 (pm20) cc_final: 0.6984 (pt0) REVERT: B 362 LEU cc_start: 0.9152 (mt) cc_final: 0.8916 (mp) REVERT: B 436 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8022 (mmp80) REVERT: B 450 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6979 (mp) REVERT: B 451 PHE cc_start: 0.7670 (p90) cc_final: 0.7438 (p90) REVERT: B 481 MET cc_start: 0.7048 (ptm) cc_final: 0.6793 (ptm) REVERT: B 602 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6764 (p90) REVERT: B 604 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8596 (pp30) REVERT: B 707 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7769 (mmm160) outliers start: 95 outliers final: 72 residues processed: 552 average time/residue: 0.2568 time to fit residues: 216.0129 Evaluate side-chains 563 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 483 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 581 LYS Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 602 PHE Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 427 optimal weight: 9.9990 chunk 319 optimal weight: 0.6980 chunk 387 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 395 optimal weight: 2.9990 chunk 409 optimal weight: 0.9980 chunk 442 optimal weight: 9.9990 chunk 475 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 406 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.078750 restraints weight = 98844.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.080752 restraints weight = 51941.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.082163 restraints weight = 35920.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082818 restraints weight = 27845.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.083395 restraints weight = 24435.948| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39065 Z= 0.135 Angle : 0.643 17.120 52958 Z= 0.320 Chirality : 0.043 0.203 6154 Planarity : 0.005 0.064 6811 Dihedral : 8.358 89.704 5618 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 1.93 % Allowed : 17.98 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.13), residues: 4863 helix: 1.10 (0.11), residues: 2235 sheet: 0.70 (0.21), residues: 617 loop : -1.53 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 538 TYR 0.018 0.001 TYR B 324 PHE 0.027 0.001 PHE D 451 TRP 0.020 0.001 TRP G 90 HIS 0.004 0.001 HIS F 655 Details of bonding type rmsd covalent geometry : bond 0.00299 (39065) covalent geometry : angle 0.64332 (52958) hydrogen bonds : bond 0.06195 ( 1554) hydrogen bonds : angle 4.28244 ( 4614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 499 time to evaluate : 1.272 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 57 ASP cc_start: 0.8423 (t0) cc_final: 0.8027 (t0) REVERT: A 153 MET cc_start: 0.8690 (ptm) cc_final: 0.8400 (ppp) REVERT: A 481 MET cc_start: 0.8841 (mtm) cc_final: 0.8498 (mtp) REVERT: A 501 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8094 (ptp-170) REVERT: A 710 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7968 (tpp80) REVERT: A 811 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8106 (t-170) REVERT: J 24 LYS cc_start: 0.8601 (pttp) cc_final: 0.8306 (ptpp) REVERT: J 117 LYS cc_start: 0.8961 (tppt) cc_final: 0.8313 (tppt) REVERT: J 146 TYR cc_start: 0.8486 (t80) cc_final: 0.8022 (t80) REVERT: I 29 ASP cc_start: 0.8015 (m-30) cc_final: 0.7710 (m-30) REVERT: I 117 LYS cc_start: 0.8791 (tptm) cc_final: 0.8441 (tptt) REVERT: I 121 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7245 (mp0) REVERT: H 133 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: H 216 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (mp) REVERT: F 109 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: F 221 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7344 (ttp80) REVERT: F 372 LYS cc_start: 0.8948 (tptt) cc_final: 0.8734 (tmtt) REVERT: F 403 TYR cc_start: 0.8365 (m-10) cc_final: 0.8078 (m-10) REVERT: F 417 MET cc_start: 0.8737 (tpp) cc_final: 0.8366 (tpt) REVERT: F 543 GLU cc_start: 0.7443 (mp0) cc_final: 0.7196 (mp0) REVERT: F 620 ARG cc_start: 0.7123 (mmm160) cc_final: 0.6828 (tpm170) REVERT: E 75 MET cc_start: 0.8190 (tpt) cc_final: 0.7819 (tpt) REVERT: E 201 MET cc_start: 0.6443 (mtm) cc_final: 0.6191 (mtm) REVERT: E 393 TYR cc_start: 0.7048 (m-80) cc_final: 0.6339 (m-80) REVERT: E 735 GLU cc_start: 0.6879 (pp20) cc_final: 0.6457 (pp20) REVERT: C 280 GLU cc_start: 0.8484 (tp30) cc_final: 0.8278 (tp30) REVERT: C 284 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8007 (mtm110) REVERT: C 286 PHE cc_start: 0.8744 (m-80) cc_final: 0.8256 (m-80) REVERT: C 290 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8058 (tpp80) REVERT: C 304 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: C 372 LYS cc_start: 0.8430 (tptp) cc_final: 0.7953 (tptp) REVERT: C 544 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8355 (mmmt) REVERT: C 742 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 75 MET cc_start: 0.7392 (ppp) cc_final: 0.6717 (mpp) REVERT: B 144 MET cc_start: 0.5998 (tmm) cc_final: 0.5680 (tmm) REVERT: B 201 MET cc_start: 0.8494 (ppp) cc_final: 0.8089 (ppp) REVERT: B 331 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8058 (mtm-85) REVERT: B 361 GLN cc_start: 0.7714 (pm20) cc_final: 0.6992 (pt0) REVERT: B 362 LEU cc_start: 0.9117 (mt) cc_final: 0.8904 (mp) REVERT: B 436 ARG cc_start: 0.8702 (mmp80) cc_final: 0.8154 (mmp80) REVERT: B 481 MET cc_start: 0.7064 (ptm) cc_final: 0.6805 (ptm) REVERT: B 604 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8692 (pp30) REVERT: B 707 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7766 (mmm160) outliers start: 80 outliers final: 57 residues processed: 551 average time/residue: 0.2505 time to fit residues: 211.7504 Evaluate side-chains 552 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 488 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 443 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 485 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 457 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 503 HIS ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS E 361 GLN ** E 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.105359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.076324 restraints weight = 99405.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.078225 restraints weight = 52519.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.079615 restraints weight = 36708.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.080212 restraints weight = 28556.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.080883 restraints weight = 25105.308| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 39065 Z= 0.200 Angle : 0.709 16.690 52958 Z= 0.354 Chirality : 0.046 0.191 6154 Planarity : 0.005 0.061 6811 Dihedral : 8.524 88.541 5618 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 2.07 % Allowed : 17.94 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4863 helix: 0.94 (0.11), residues: 2228 sheet: 0.68 (0.21), residues: 612 loop : -1.57 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 366 TYR 0.016 0.002 TYR A 393 PHE 0.027 0.002 PHE D 451 TRP 0.018 0.002 TRP G 90 HIS 0.008 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00472 (39065) covalent geometry : angle 0.70876 (52958) hydrogen bonds : bond 0.07442 ( 1554) hydrogen bonds : angle 4.47665 ( 4614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 505 time to evaluate : 1.205 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 57 ASP cc_start: 0.8473 (t0) cc_final: 0.8047 (t0) REVERT: A 153 MET cc_start: 0.8727 (ptm) cc_final: 0.8448 (ppp) REVERT: A 501 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8149 (ptp-170) REVERT: A 811 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (t-170) REVERT: J 24 LYS cc_start: 0.8592 (pttp) cc_final: 0.8280 (ptpp) REVERT: J 85 ASN cc_start: 0.6805 (p0) cc_final: 0.6401 (p0) REVERT: J 117 LYS cc_start: 0.9057 (tppt) cc_final: 0.8536 (tppt) REVERT: J 146 TYR cc_start: 0.8644 (t80) cc_final: 0.8256 (t80) REVERT: H 216 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (mp) REVERT: F 109 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7569 (mtm-85) REVERT: F 214 GLU cc_start: 0.8463 (pp20) cc_final: 0.8170 (pp20) REVERT: F 221 ARG cc_start: 0.8090 (ptm-80) cc_final: 0.7627 (ttp80) REVERT: F 372 LYS cc_start: 0.8974 (tptt) cc_final: 0.8707 (tptp) REVERT: F 543 GLU cc_start: 0.7502 (mp0) cc_final: 0.7237 (mp0) REVERT: E 75 MET cc_start: 0.8275 (tpt) cc_final: 0.7937 (tpt) REVERT: E 201 MET cc_start: 0.6525 (mtm) cc_final: 0.6266 (mtm) REVERT: E 393 TYR cc_start: 0.7146 (m-80) cc_final: 0.6368 (m-80) REVERT: E 735 GLU cc_start: 0.6906 (pp20) cc_final: 0.6477 (pp20) REVERT: C 229 LEU cc_start: 0.8616 (pt) cc_final: 0.8331 (pp) REVERT: C 280 GLU cc_start: 0.8579 (tp30) cc_final: 0.8316 (tp30) REVERT: C 284 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7930 (mtm110) REVERT: C 304 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: C 372 LYS cc_start: 0.8333 (tptp) cc_final: 0.7955 (tptp) REVERT: C 544 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8453 (mmmt) REVERT: C 742 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: B 75 MET cc_start: 0.7418 (ppp) cc_final: 0.6804 (mpp) REVERT: B 144 MET cc_start: 0.6120 (tmm) cc_final: 0.5780 (tmm) REVERT: B 201 MET cc_start: 0.8460 (ppp) cc_final: 0.8177 (ppp) REVERT: B 436 ARG cc_start: 0.8689 (mmp80) cc_final: 0.8167 (mmp80) REVERT: B 481 MET cc_start: 0.7045 (ptm) cc_final: 0.6788 (ptm) REVERT: B 537 LEU cc_start: 0.8842 (tp) cc_final: 0.8511 (tp) REVERT: B 707 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7822 (mmm160) outliers start: 86 outliers final: 65 residues processed: 559 average time/residue: 0.2501 time to fit residues: 212.7001 Evaluate side-chains 560 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 489 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 581 LYS Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 336 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 432 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 364 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 481 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 402 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 426 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 454 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.076825 restraints weight = 98750.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.078800 restraints weight = 52162.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.080147 restraints weight = 36173.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.081138 restraints weight = 28352.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.081514 restraints weight = 23711.420| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39065 Z= 0.172 Angle : 0.703 19.587 52958 Z= 0.351 Chirality : 0.045 0.203 6154 Planarity : 0.005 0.093 6811 Dihedral : 8.395 89.586 5614 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 1.83 % Allowed : 18.59 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.12), residues: 4863 helix: 1.01 (0.11), residues: 2225 sheet: 0.74 (0.21), residues: 610 loop : -1.55 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 538 TYR 0.014 0.001 TYR I 84 PHE 0.029 0.001 PHE D 451 TRP 0.020 0.001 TRP G 90 HIS 0.006 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00398 (39065) covalent geometry : angle 0.70276 (52958) hydrogen bonds : bond 0.06952 ( 1554) hydrogen bonds : angle 4.42737 ( 4614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 496 time to evaluate : 1.006 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: A 54 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8875 (mmmt) REVERT: A 57 ASP cc_start: 0.8479 (t0) cc_final: 0.8042 (t0) REVERT: A 153 MET cc_start: 0.8687 (ptm) cc_final: 0.8423 (ppp) REVERT: A 501 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8115 (ptp-170) REVERT: A 811 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8093 (t-170) REVERT: J 24 LYS cc_start: 0.8593 (pttp) cc_final: 0.8276 (ptpp) REVERT: J 94 GLU cc_start: 0.7820 (pp20) cc_final: 0.7406 (pp20) REVERT: J 117 LYS cc_start: 0.9061 (tppt) cc_final: 0.8614 (tppt) REVERT: J 146 TYR cc_start: 0.8627 (t80) cc_final: 0.8256 (t80) REVERT: H 216 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8273 (mp) REVERT: F 109 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: F 214 GLU cc_start: 0.8473 (pp20) cc_final: 0.8135 (pp20) REVERT: F 372 LYS cc_start: 0.8960 (tptt) cc_final: 0.8674 (tptp) REVERT: F 417 MET cc_start: 0.8707 (tpp) cc_final: 0.8311 (tpt) REVERT: F 543 GLU cc_start: 0.7490 (mp0) cc_final: 0.7217 (mp0) REVERT: E 75 MET cc_start: 0.8250 (tpt) cc_final: 0.7916 (tpt) REVERT: E 393 TYR cc_start: 0.7162 (m-80) cc_final: 0.6442 (m-80) REVERT: E 735 GLU cc_start: 0.6876 (pp20) cc_final: 0.6434 (pp20) REVERT: D 180 TYR cc_start: 0.7190 (t80) cc_final: 0.6956 (t80) REVERT: D 439 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6808 (t80) REVERT: D 494 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8459 (tt) REVERT: D 710 ARG cc_start: 0.6964 (ttm-80) cc_final: 0.6756 (ttm-80) REVERT: C 229 LEU cc_start: 0.8606 (pt) cc_final: 0.8335 (pp) REVERT: C 280 GLU cc_start: 0.8599 (tp30) cc_final: 0.8356 (tp30) REVERT: C 290 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8058 (tpp80) REVERT: C 304 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: C 372 LYS cc_start: 0.8296 (tptp) cc_final: 0.7943 (tptp) REVERT: C 544 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8447 (mmmt) REVERT: C 742 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: B 75 MET cc_start: 0.7407 (ppp) cc_final: 0.6784 (mpp) REVERT: B 144 MET cc_start: 0.6079 (tmm) cc_final: 0.5725 (tmm) REVERT: B 201 MET cc_start: 0.8411 (ppp) cc_final: 0.8145 (ppp) REVERT: B 436 ARG cc_start: 0.8649 (mmp80) cc_final: 0.8138 (mmp80) REVERT: B 481 MET cc_start: 0.7062 (ptm) cc_final: 0.6806 (ptm) REVERT: B 537 LEU cc_start: 0.8867 (tp) cc_final: 0.8541 (tp) REVERT: B 707 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7837 (mmm160) outliers start: 76 outliers final: 65 residues processed: 549 average time/residue: 0.2491 time to fit residues: 208.2584 Evaluate side-chains 562 residues out of total 4148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 489 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 811 HIS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 499 LYS Chi-restraints excluded: chain F residue 566 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain E residue 529 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 811 HIS Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 460 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.076404 restraints weight = 100158.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.078465 restraints weight = 53534.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.079898 restraints weight = 36877.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.080454 restraints weight = 28882.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.081084 restraints weight = 25561.718| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39065 Z= 0.172 Angle : 0.700 19.800 52958 Z= 0.349 Chirality : 0.045 0.185 6154 Planarity : 0.005 0.077 6811 Dihedral : 8.296 89.519 5614 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 2.03 % Allowed : 18.61 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.12), residues: 4863 helix: 1.04 (0.11), residues: 2221 sheet: 0.75 (0.21), residues: 611 loop : -1.52 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 538 TYR 0.014 0.001 TYR I 146 PHE 0.029 0.001 PHE D 451 TRP 0.020 0.001 TRP G 90 HIS 0.006 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00398 (39065) covalent geometry : angle 0.69989 (52958) hydrogen bonds : bond 0.06903 ( 1554) hydrogen bonds : angle 4.40636 ( 4614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5462.81 seconds wall clock time: 95 minutes 10.14 seconds (5710.14 seconds total)