Starting phenix.real_space_refine on Thu Mar 21 09:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqv_7133/03_2024/6bqv_7133_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19268 2.51 5 N 5148 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 415": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 1064": "NH1" <-> "NH2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 770": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 955": "NH1" <-> "NH2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B ARG 1067": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 415": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C ARG 770": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 1064": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 415": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 767": "NH1" <-> "NH2" Residue "D ARG 770": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 955": "NH1" <-> "NH2" Residue "D ARG 1064": "NH1" <-> "NH2" Residue "D ARG 1067": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29716 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 15.68, per 1000 atoms: 0.53 Number of scatterers: 29716 At special positions: 0 Unit cell: (139.118, 139.118, 160.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5144 8.00 N 5148 7.00 C 19268 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 - 3.50 Amino acid : False - 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: 11.74 Conformation dependent library (CDL) restraints added in 5.1 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6896 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 16 sheets defined 67.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 571 through 579 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.796A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 removed outlier: 3.524A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 804 Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.518A pdb=" N ARG A 830 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1031 Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.527A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 3.562A pdb=" N ALA A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1165 " --> pdb=" O GLN A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU A1175 " --> pdb=" O ARG A1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 3.686A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.505A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.524A pdb=" N GLN B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.797A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 removed outlier: 3.525A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 705 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 804 Processing helix chain 'B' and resid 811 through 830 removed outlier: 3.519A pdb=" N ARG B 830 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 3.505A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1094 removed outlier: 3.527A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU B1175 " --> pdb=" O ARG B1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 339 removed outlier: 3.591A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU C 381 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 571 through 579 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.689A pdb=" N LEU C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN C 678 " --> pdb=" O SER C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.796A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 removed outlier: 3.524A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 705 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE C 775 " --> pdb=" O ARG C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 804 Processing helix chain 'C' and resid 811 through 830 removed outlier: 3.519A pdb=" N ARG C 830 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 926 through 952 removed outlier: 3.523A pdb=" N PHE C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C1068 " --> pdb=" O ARG C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1094 removed outlier: 3.528A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1165 " --> pdb=" O GLN C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR D 103 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.018A pdb=" N THR D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.686A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.577A pdb=" N ARG D 601 " --> pdb=" O ARG D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 616 " --> pdb=" O ARG D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU D 641 " --> pdb=" O ARG D 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.795A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.525A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 705 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 804 Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.518A pdb=" N ARG D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 removed outlier: 3.566A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.955A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1031 Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D1060 " --> pdb=" O LEU D1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D1068 " --> pdb=" O ARG D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1094 removed outlier: 3.528A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1167 removed outlier: 3.957A pdb=" N HIS D1164 " --> pdb=" O LYS D1160 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D1165 " --> pdb=" O GLN D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU D1175 " --> pdb=" O ARG D1171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL A 119 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'A' and resid 1000 through 1001 Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.934A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL B 119 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AA8, first strand: chain 'B' and resid 1000 through 1001 Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL C 119 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB3, first strand: chain 'C' and resid 1000 through 1001 Processing sheet with id=AB4, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL D 119 " --> pdb=" O TRP D 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AB7, first strand: chain 'D' and resid 1000 through 1001 1544 hydrogen bonds defined for protein. 4572 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: 9.72 Time building geometry restraints manager: 12.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4666 1.31 - 1.43: 8280 1.43 - 1.56: 17050 1.56 - 1.69: 148 1.69 - 1.81: 248 Bond restraints: 30392 Sorted by residual: bond pdb=" CAI Y01 A1302 " pdb=" CAZ Y01 A1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.02e+02 bond pdb=" CAI Y01 D1302 " pdb=" CAZ Y01 D1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" CAI Y01 B1302 " pdb=" CAZ Y01 B1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.00e+02 bond pdb=" CAI Y01 C1302 " pdb=" CAZ Y01 C1302 " ideal model delta sigma weight residual 1.332 1.678 -0.346 2.00e-02 2.50e+03 3.00e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.675 -0.343 2.00e-02 2.50e+03 2.94e+02 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.71: 549 104.71 - 112.39: 15044 112.39 - 120.08: 12684 120.08 - 127.77: 12597 127.77 - 135.46: 362 Bond angle restraints: 41236 Sorted by residual: angle pdb=" C ALA A1076 " pdb=" N PRO A1077 " pdb=" CA PRO A1077 " ideal model delta sigma weight residual 120.38 133.32 -12.94 1.03e+00 9.43e-01 1.58e+02 angle pdb=" C ALA C1076 " pdb=" N PRO C1077 " pdb=" CA PRO C1077 " ideal model delta sigma weight residual 120.38 133.31 -12.93 1.03e+00 9.43e-01 1.58e+02 angle pdb=" C ALA D1076 " pdb=" N PRO D1077 " pdb=" CA PRO D1077 " ideal model delta sigma weight residual 120.38 133.30 -12.92 1.03e+00 9.43e-01 1.57e+02 angle pdb=" C ALA B1076 " pdb=" N PRO B1077 " pdb=" CA PRO B1077 " ideal model delta sigma weight residual 120.38 133.30 -12.92 1.03e+00 9.43e-01 1.57e+02 angle pdb=" N PRO D1077 " pdb=" CA PRO D1077 " pdb=" C PRO D1077 " ideal model delta sigma weight residual 110.70 119.19 -8.49 1.22e+00 6.72e-01 4.84e+01 ... (remaining 41231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 16833 17.35 - 34.69: 1255 34.69 - 52.04: 352 52.04 - 69.38: 68 69.38 - 86.73: 32 Dihedral angle restraints: 18540 sinusoidal: 7864 harmonic: 10676 Sorted by residual: dihedral pdb=" CA LEU D 707 " pdb=" C LEU D 707 " pdb=" N ILE D 708 " pdb=" CA ILE D 708 " ideal model delta harmonic sigma weight residual 180.00 -131.35 -48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA LEU B 707 " pdb=" C LEU B 707 " pdb=" N ILE B 708 " pdb=" CA ILE B 708 " ideal model delta harmonic sigma weight residual 180.00 -131.40 -48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" CA LEU A 707 " pdb=" C LEU A 707 " pdb=" N ILE A 708 " pdb=" CA ILE A 708 " ideal model delta harmonic sigma weight residual -180.00 -131.41 -48.59 0 5.00e+00 4.00e-02 9.44e+01 ... (remaining 18537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4263 0.103 - 0.205: 334 0.205 - 0.308: 39 0.308 - 0.411: 16 0.411 - 0.514: 8 Chirality restraints: 4660 Sorted by residual: chirality pdb=" CBI Y01 C1303 " pdb=" CAU Y01 C1303 " pdb=" CBE Y01 C1303 " pdb=" CBG Y01 C1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CBI Y01 A1303 " pdb=" CAU Y01 A1303 " pdb=" CBE Y01 A1303 " pdb=" CBG Y01 A1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CBI Y01 B1303 " pdb=" CAU Y01 B1303 " pdb=" CBE Y01 B1303 " pdb=" CBG Y01 B1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 4657 not shown) Planarity restraints: 5152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " 0.043 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP C 152 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " -0.043 2.00e-02 2.50e+03 2.84e-02 2.02e+01 pdb=" CG TRP A 152 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " 0.043 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP D 152 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " 0.009 2.00e-02 2.50e+03 ... (remaining 5149 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 41 1.96 - 2.69: 1064 2.69 - 3.43: 43046 3.43 - 4.16: 73198 4.16 - 4.90: 128136 Nonbonded interactions: 245485 Sorted by model distance: nonbonded pdb=" NH2 ARG B1166 " pdb=" CG HIS D1164 " model vdw 1.221 3.340 nonbonded pdb=" CG HIS A1164 " pdb=" NH2 ARG C1166 " model vdw 1.255 3.340 nonbonded pdb=" CG HIS C1164 " pdb=" NH2 ARG D1166 " model vdw 1.324 3.340 nonbonded pdb=" NH2 ARG A1166 " pdb=" CG HIS B1164 " model vdw 1.354 3.340 nonbonded pdb=" OD2 ASP B 172 " pdb=" CZ PHE D 414 " model vdw 1.462 3.340 ... (remaining 245480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.250 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 74.440 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.014 0.347 30392 Z= 0.848 Angle : 1.370 19.159 41236 Z= 0.701 Chirality : 0.068 0.514 4660 Planarity : 0.008 0.075 5152 Dihedral : 14.129 86.727 11644 Min Nonbonded Distance : 1.221 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.57 % Favored : 91.21 % Rotamer: Outliers : 3.54 % Allowed : 8.58 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.09), residues: 3640 helix: -3.64 (0.06), residues: 2340 sheet: -4.91 (0.20), residues: 216 loop : -3.43 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP C 152 HIS 0.018 0.003 HIS C 774 PHE 0.035 0.004 PHE C 710 TYR 0.033 0.003 TYR A 227 ARG 0.017 0.001 ARG C 964 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 764 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6177 (tm) REVERT: A 254 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 355 MET cc_start: 0.4310 (tpp) cc_final: 0.3947 (mmm) REVERT: A 462 GLN cc_start: 0.8528 (tp40) cc_final: 0.8265 (tp-100) REVERT: A 559 TRP cc_start: 0.8305 (m100) cc_final: 0.7899 (m100) REVERT: A 588 SER cc_start: 0.9171 (m) cc_final: 0.8961 (m) REVERT: A 620 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7655 (tt0) REVERT: A 629 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 635 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7807 (mp0) REVERT: A 659 MET cc_start: 0.7429 (ttm) cc_final: 0.7043 (ttp) REVERT: A 662 ASP cc_start: 0.7502 (t0) cc_final: 0.7277 (t0) REVERT: A 856 LEU cc_start: 0.8130 (mp) cc_final: 0.7892 (mp) REVERT: A 877 LEU cc_start: 0.8777 (mp) cc_final: 0.8127 (tt) REVERT: A 983 MET cc_start: 0.8868 (mtm) cc_final: 0.8509 (mtm) REVERT: A 984 ASP cc_start: 0.8819 (t0) cc_final: 0.8532 (t0) REVERT: A 1032 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8523 (m110) REVERT: A 1056 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 1063 TYR cc_start: 0.8837 (t80) cc_final: 0.8530 (t80) REVERT: A 1067 ARG cc_start: 0.7912 (ptm-80) cc_final: 0.7604 (ptm-80) REVERT: A 1118 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 1140 LYS cc_start: 0.8702 (tttt) cc_final: 0.8396 (tttp) REVERT: A 1154 LYS cc_start: 0.8135 (mttt) cc_final: 0.7909 (mtmt) REVERT: A 1168 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6101 (m-10) REVERT: B 355 MET cc_start: 0.4497 (tpp) cc_final: 0.4171 (mmm) REVERT: B 436 ASP cc_start: 0.7549 (t70) cc_final: 0.7317 (t70) REVERT: B 462 GLN cc_start: 0.8551 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 588 SER cc_start: 0.9242 (m) cc_final: 0.9021 (m) REVERT: B 608 GLU cc_start: 0.6934 (tp30) cc_final: 0.5451 (mm-30) REVERT: B 620 GLU cc_start: 0.8697 (mm-30) cc_final: 0.7445 (tt0) REVERT: B 629 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 635 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7693 (mp0) REVERT: B 659 MET cc_start: 0.7470 (ttm) cc_final: 0.7158 (ttp) REVERT: B 711 ARG cc_start: 0.6607 (mpt-90) cc_final: 0.6007 (ptm-80) REVERT: B 852 LEU cc_start: 0.7014 (mm) cc_final: 0.6748 (mt) REVERT: B 856 LEU cc_start: 0.8105 (mp) cc_final: 0.7819 (mp) REVERT: B 877 LEU cc_start: 0.8788 (mp) cc_final: 0.8157 (tt) REVERT: B 915 GLN cc_start: 0.7882 (tt0) cc_final: 0.7573 (mp10) REVERT: B 983 MET cc_start: 0.8901 (mtm) cc_final: 0.8625 (mtm) REVERT: B 1032 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8498 (m110) REVERT: B 1056 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8035 (mp) REVERT: B 1063 TYR cc_start: 0.8949 (t80) cc_final: 0.8739 (t80) REVERT: B 1067 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7735 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8528 (tt) cc_final: 0.8327 (tt) REVERT: B 1115 LYS cc_start: 0.7952 (tppp) cc_final: 0.7649 (mmtt) REVERT: B 1140 LYS cc_start: 0.8677 (tttt) cc_final: 0.8417 (tttp) REVERT: B 1149 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8376 (mtpt) REVERT: B 1154 LYS cc_start: 0.8107 (mttt) cc_final: 0.7867 (mtmt) REVERT: B 1168 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6182 (m-10) REVERT: C 251 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6177 (tm) REVERT: C 254 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6912 (mt-10) REVERT: C 355 MET cc_start: 0.4313 (tpp) cc_final: 0.3950 (mmm) REVERT: C 405 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.7281 (ttt90) REVERT: C 462 GLN cc_start: 0.8547 (tp40) cc_final: 0.8286 (tp-100) REVERT: C 559 TRP cc_start: 0.8309 (m100) cc_final: 0.7885 (m100) REVERT: C 588 SER cc_start: 0.9171 (m) cc_final: 0.8960 (m) REVERT: C 608 GLU cc_start: 0.6968 (tp30) cc_final: 0.5690 (mm-30) REVERT: C 620 GLU cc_start: 0.8736 (mm-30) cc_final: 0.7653 (tt0) REVERT: C 629 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 635 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7800 (mp0) REVERT: C 659 MET cc_start: 0.7469 (ttm) cc_final: 0.7065 (ttp) REVERT: C 662 ASP cc_start: 0.7467 (t0) cc_final: 0.7236 (t0) REVERT: C 711 ARG cc_start: 0.6566 (mpt-90) cc_final: 0.5977 (ptm-80) REVERT: C 856 LEU cc_start: 0.8126 (mp) cc_final: 0.7906 (mp) REVERT: C 877 LEU cc_start: 0.8778 (mp) cc_final: 0.8123 (tt) REVERT: C 915 GLN cc_start: 0.7969 (tt0) cc_final: 0.7595 (mp10) REVERT: C 983 MET cc_start: 0.8846 (mtm) cc_final: 0.8481 (mtm) REVERT: C 1032 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8500 (m110) REVERT: C 1056 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 1063 TYR cc_start: 0.8844 (t80) cc_final: 0.8544 (t80) REVERT: C 1067 ARG cc_start: 0.7905 (ptm-80) cc_final: 0.7596 (ptm-80) REVERT: C 1115 LYS cc_start: 0.8032 (tppp) cc_final: 0.7734 (mmtt) REVERT: C 1140 LYS cc_start: 0.8708 (tttt) cc_final: 0.8405 (tttp) REVERT: C 1154 LYS cc_start: 0.8109 (mttt) cc_final: 0.7891 (mtmt) REVERT: C 1168 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6175 (m-10) REVERT: D 251 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6059 (tm) REVERT: D 254 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6818 (mt-10) REVERT: D 355 MET cc_start: 0.4191 (tpp) cc_final: 0.3955 (mmm) REVERT: D 405 ARG cc_start: 0.7507 (tpt-90) cc_final: 0.7288 (ttt90) REVERT: D 462 GLN cc_start: 0.8480 (tp40) cc_final: 0.8098 (tp-100) REVERT: D 559 TRP cc_start: 0.8294 (m100) cc_final: 0.7869 (m100) REVERT: D 588 SER cc_start: 0.9130 (m) cc_final: 0.8918 (m) REVERT: D 612 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8250 (tpp-160) REVERT: D 620 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7614 (tt0) REVERT: D 629 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 635 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7788 (mp0) REVERT: D 659 MET cc_start: 0.7408 (ttm) cc_final: 0.6995 (ttp) REVERT: D 662 ASP cc_start: 0.7512 (t0) cc_final: 0.7305 (t0) REVERT: D 711 ARG cc_start: 0.6384 (mpt-90) cc_final: 0.5864 (ptm-80) REVERT: D 856 LEU cc_start: 0.8127 (mp) cc_final: 0.7893 (mp) REVERT: D 877 LEU cc_start: 0.8779 (mp) cc_final: 0.8144 (tt) REVERT: D 983 MET cc_start: 0.8867 (mtm) cc_final: 0.8506 (mtm) REVERT: D 1032 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8540 (m110) REVERT: D 1045 TYR cc_start: 0.8707 (t80) cc_final: 0.8499 (t80) REVERT: D 1056 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8063 (mp) REVERT: D 1063 TYR cc_start: 0.8855 (t80) cc_final: 0.8520 (t80) REVERT: D 1067 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7562 (ptm-80) REVERT: D 1118 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 1140 LYS cc_start: 0.8682 (tttt) cc_final: 0.8384 (tttp) REVERT: D 1154 LYS cc_start: 0.8043 (mttt) cc_final: 0.7830 (mtmt) REVERT: D 1168 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6109 (m-10) outliers start: 108 outliers final: 47 residues processed: 849 average time/residue: 0.4946 time to fit residues: 616.7638 Evaluate side-chains 577 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 515 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 830 ARG Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1166 ARG Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1166 ARG Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1166 ARG Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 291 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 337 optimal weight: 0.0020 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 173 HIS ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 348 GLN A 419 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 977 GLN A1061 GLN A1084 HIS A1128 HIS B 116 ASN B 173 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 419 GLN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B1037 ASN B1061 GLN B1084 HIS B1128 HIS B1161 GLN B1170 GLN C 116 ASN C 173 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 348 GLN C 419 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 GLN C 977 GLN C1014 GLN C1061 GLN C1084 HIS C1128 HIS C1131 ASN D 116 ASN D 173 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 348 GLN D 419 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 GLN D 977 GLN D1014 GLN D1037 ASN D1061 GLN D1084 HIS D1128 HIS D1161 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30392 Z= 0.242 Angle : 0.737 9.884 41236 Z= 0.362 Chirality : 0.041 0.266 4660 Planarity : 0.007 0.059 5152 Dihedral : 9.530 59.640 5055 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.98 % Allowed : 13.63 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.12), residues: 3640 helix: -1.68 (0.09), residues: 2412 sheet: -4.57 (0.22), residues: 200 loop : -3.01 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 152 HIS 0.008 0.001 HIS C 774 PHE 0.028 0.002 PHE A 414 TYR 0.012 0.001 TYR B 227 ARG 0.007 0.001 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 606 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ILE cc_start: 0.6958 (tp) cc_final: 0.6750 (tp) REVERT: A 260 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6936 (mt0) REVERT: A 355 MET cc_start: 0.4570 (tpp) cc_final: 0.4039 (mmm) REVERT: A 410 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: A 588 SER cc_start: 0.9022 (m) cc_final: 0.8750 (m) REVERT: A 611 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7245 (mtm110) REVERT: A 629 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 659 MET cc_start: 0.7539 (ttm) cc_final: 0.7004 (ttp) REVERT: A 770 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6804 (ttp80) REVERT: A 827 GLU cc_start: 0.7577 (tp30) cc_final: 0.6951 (tp30) REVERT: A 1015 TYR cc_start: 0.8370 (t80) cc_final: 0.7857 (t80) REVERT: A 1032 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8569 (m110) REVERT: A 1056 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 1063 TYR cc_start: 0.8877 (t80) cc_final: 0.8442 (t80) REVERT: A 1077 PRO cc_start: 0.7542 (Cg_exo) cc_final: 0.7098 (Cg_endo) REVERT: A 1154 LYS cc_start: 0.8113 (mttt) cc_final: 0.7869 (mtpt) REVERT: B 355 MET cc_start: 0.4801 (tpp) cc_final: 0.4318 (mmm) REVERT: B 410 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: B 462 GLN cc_start: 0.8438 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 588 SER cc_start: 0.9077 (m) cc_final: 0.8782 (m) REVERT: B 599 MET cc_start: 0.8071 (ptm) cc_final: 0.7604 (ptm) REVERT: B 659 MET cc_start: 0.7630 (ttm) cc_final: 0.7045 (ttp) REVERT: B 711 ARG cc_start: 0.6499 (mpt-90) cc_final: 0.6043 (ptm-80) REVERT: B 819 PHE cc_start: 0.8666 (t80) cc_final: 0.8445 (t80) REVERT: B 827 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: B 852 LEU cc_start: 0.7333 (mm) cc_final: 0.7103 (mt) REVERT: B 915 GLN cc_start: 0.8118 (tt0) cc_final: 0.7914 (mp10) REVERT: B 1015 TYR cc_start: 0.8396 (t80) cc_final: 0.7948 (t80) REVERT: B 1032 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8544 (m110) REVERT: B 1056 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 1063 TYR cc_start: 0.8910 (t80) cc_final: 0.8418 (t80) REVERT: B 1080 ILE cc_start: 0.8467 (tt) cc_final: 0.8166 (tt) REVERT: C 257 ILE cc_start: 0.6955 (tp) cc_final: 0.6730 (tp) REVERT: C 260 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: C 355 MET cc_start: 0.4575 (tpp) cc_final: 0.4043 (mmm) REVERT: C 410 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: C 588 SER cc_start: 0.9010 (m) cc_final: 0.8724 (m) REVERT: C 629 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 659 MET cc_start: 0.7551 (ttm) cc_final: 0.7048 (ttp) REVERT: C 770 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6750 (ttp80) REVERT: C 827 GLU cc_start: 0.7582 (tp30) cc_final: 0.6954 (tp30) REVERT: C 852 LEU cc_start: 0.7238 (mm) cc_final: 0.7018 (mt) REVERT: C 915 GLN cc_start: 0.8145 (tt0) cc_final: 0.7919 (mp10) REVERT: C 1015 TYR cc_start: 0.8388 (t80) cc_final: 0.7853 (t80) REVERT: C 1032 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8568 (m110) REVERT: C 1056 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7988 (mp) REVERT: C 1063 TYR cc_start: 0.8865 (t80) cc_final: 0.8453 (t80) REVERT: C 1077 PRO cc_start: 0.7545 (Cg_exo) cc_final: 0.7101 (Cg_endo) REVERT: C 1154 LYS cc_start: 0.8111 (mttt) cc_final: 0.7878 (mtpt) REVERT: D 257 ILE cc_start: 0.6927 (tp) cc_final: 0.6696 (tp) REVERT: D 260 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: D 355 MET cc_start: 0.4547 (tpp) cc_final: 0.4254 (mmm) REVERT: D 410 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: D 574 MET cc_start: 0.8396 (mmm) cc_final: 0.7901 (mmt) REVERT: D 578 PHE cc_start: 0.9276 (m-10) cc_final: 0.8984 (m-80) REVERT: D 588 SER cc_start: 0.9038 (m) cc_final: 0.8771 (m) REVERT: D 611 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7214 (mtm110) REVERT: D 659 MET cc_start: 0.7516 (ttm) cc_final: 0.7045 (ttp) REVERT: D 770 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6800 (ttp80) REVERT: D 827 GLU cc_start: 0.7453 (tp30) cc_final: 0.7031 (tp30) REVERT: D 1015 TYR cc_start: 0.8375 (t80) cc_final: 0.7837 (t80) REVERT: D 1032 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8573 (m110) REVERT: D 1056 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7967 (mp) REVERT: D 1063 TYR cc_start: 0.8866 (t80) cc_final: 0.8490 (t80) REVERT: D 1077 PRO cc_start: 0.7559 (Cg_exo) cc_final: 0.7101 (Cg_endo) outliers start: 152 outliers final: 59 residues processed: 711 average time/residue: 0.4277 time to fit residues: 469.2328 Evaluate side-chains 592 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 517 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1166 ARG Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1166 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 0.2980 chunk 365 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN A1061 GLN A1084 HIS A1131 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B1061 GLN B1084 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN C1061 GLN C1084 HIS ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN D1061 GLN D1084 HIS D1164 HIS D1170 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30392 Z= 0.446 Angle : 0.829 9.979 41236 Z= 0.399 Chirality : 0.046 0.276 4660 Planarity : 0.006 0.075 5152 Dihedral : 8.776 59.974 4961 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.68 % Allowed : 14.09 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3640 helix: -0.83 (0.10), residues: 2404 sheet: -4.18 (0.27), residues: 192 loop : -3.04 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 152 HIS 0.008 0.002 HIS B 908 PHE 0.032 0.003 PHE C 797 TYR 0.023 0.002 TYR D 464 ARG 0.008 0.001 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 538 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6608 (tpt90) REVERT: A 410 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: A 436 ASP cc_start: 0.7117 (t70) cc_final: 0.6822 (t0) REVERT: A 581 MET cc_start: 0.8264 (mmt) cc_final: 0.7910 (tpp) REVERT: A 588 SER cc_start: 0.9009 (m) cc_final: 0.8800 (m) REVERT: A 611 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7287 (mtm110) REVERT: A 711 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7527 (ptm-80) REVERT: A 876 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (tp) REVERT: A 877 LEU cc_start: 0.8818 (mp) cc_final: 0.8294 (tt) REVERT: A 972 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8926 (mt) REVERT: A 1057 TYR cc_start: 0.7541 (t80) cc_final: 0.6902 (t80) REVERT: A 1067 ARG cc_start: 0.8117 (ptm-80) cc_final: 0.7642 (ptm-80) REVERT: A 1128 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7894 (m-70) REVERT: A 1154 LYS cc_start: 0.8100 (mttt) cc_final: 0.7886 (mtpt) REVERT: B 410 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: B 581 MET cc_start: 0.8261 (mmt) cc_final: 0.7914 (tpp) REVERT: B 588 SER cc_start: 0.9034 (m) cc_final: 0.8745 (m) REVERT: B 629 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 659 MET cc_start: 0.7738 (ttm) cc_final: 0.7488 (ttp) REVERT: B 827 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7335 (tp30) REVERT: B 877 LEU cc_start: 0.8791 (mp) cc_final: 0.8255 (tt) REVERT: B 1067 ARG cc_start: 0.8128 (ptm-80) cc_final: 0.7651 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8561 (tt) cc_final: 0.8178 (tt) REVERT: B 1128 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.7856 (m-70) REVERT: B 1134 LEU cc_start: 0.8805 (mt) cc_final: 0.8484 (mm) REVERT: B 1149 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8311 (mtpt) REVERT: C 410 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: C 588 SER cc_start: 0.9070 (m) cc_final: 0.8791 (m) REVERT: C 711 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: C 852 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7189 (mt) REVERT: C 876 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8555 (tp) REVERT: C 877 LEU cc_start: 0.8817 (mp) cc_final: 0.8305 (tt) REVERT: C 926 MET cc_start: 0.9443 (mmt) cc_final: 0.9215 (mmt) REVERT: C 972 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8923 (mt) REVERT: C 1057 TYR cc_start: 0.7508 (t80) cc_final: 0.6862 (t80) REVERT: C 1067 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7642 (ptm-80) REVERT: C 1154 LYS cc_start: 0.8104 (mttt) cc_final: 0.7855 (mtmt) REVERT: D 355 MET cc_start: 0.4558 (tpp) cc_final: 0.4135 (mmm) REVERT: D 410 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: D 412 GLU cc_start: 0.7176 (tp30) cc_final: 0.6873 (tm-30) REVERT: D 611 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7195 (mtm110) REVERT: D 711 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7524 (ptm-80) REVERT: D 827 GLU cc_start: 0.7369 (tp30) cc_final: 0.6820 (tp30) REVERT: D 877 LEU cc_start: 0.8820 (mp) cc_final: 0.8297 (tt) REVERT: D 926 MET cc_start: 0.9448 (mmt) cc_final: 0.9229 (mmt) REVERT: D 972 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8932 (mt) REVERT: D 1057 TYR cc_start: 0.7548 (t80) cc_final: 0.6883 (t80) REVERT: D 1067 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7638 (ptm-80) REVERT: D 1080 ILE cc_start: 0.8564 (tt) cc_final: 0.8315 (tt) outliers start: 204 outliers final: 79 residues processed: 664 average time/residue: 0.4334 time to fit residues: 442.2635 Evaluate side-chains 599 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 504 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1128 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1166 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 711 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1166 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 321 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN B 165 HIS ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 GLN C 165 HIS ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1128 HIS D 165 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 GLN D1128 HIS D1161 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30392 Z= 0.210 Angle : 0.664 10.563 41236 Z= 0.318 Chirality : 0.040 0.260 4660 Planarity : 0.005 0.062 5152 Dihedral : 7.636 59.965 4936 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.14 % Allowed : 16.51 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3640 helix: -0.00 (0.10), residues: 2420 sheet: -3.75 (0.34), residues: 152 loop : -2.90 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 152 HIS 0.003 0.001 HIS D 774 PHE 0.021 0.001 PHE A 414 TYR 0.011 0.001 TYR B 103 ARG 0.009 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 552 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6762 (ptm-80) REVERT: A 405 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6704 (tpt170) REVERT: A 410 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: A 430 MET cc_start: 0.7600 (tmm) cc_final: 0.7341 (mmm) REVERT: A 588 SER cc_start: 0.8959 (m) cc_final: 0.8694 (m) REVERT: A 611 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7150 (mtm110) REVERT: A 711 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7524 (ptm-80) REVERT: A 770 ARG cc_start: 0.7483 (mtp85) cc_final: 0.6803 (ttp80) REVERT: A 972 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9008 (mp) REVERT: A 1015 TYR cc_start: 0.8084 (t80) cc_final: 0.7348 (t80) REVERT: A 1063 TYR cc_start: 0.9044 (t80) cc_final: 0.8613 (t80) REVERT: A 1067 ARG cc_start: 0.8015 (ptm-80) cc_final: 0.7480 (ptm-80) REVERT: A 1154 LYS cc_start: 0.8163 (mttt) cc_final: 0.7955 (mtpt) REVERT: B 144 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6893 (ptm-80) REVERT: B 410 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: B 578 PHE cc_start: 0.9289 (m-10) cc_final: 0.9063 (m-80) REVERT: B 629 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 640 ARG cc_start: 0.8434 (mtp180) cc_final: 0.8130 (mtp180) REVERT: B 659 MET cc_start: 0.7651 (ttm) cc_final: 0.7209 (ttp) REVERT: B 770 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6804 (ttp80) REVERT: B 827 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7299 (tp30) REVERT: B 963 LEU cc_start: 0.9093 (mp) cc_final: 0.8863 (mp) REVERT: B 972 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (mp) REVERT: B 1015 TYR cc_start: 0.8091 (t80) cc_final: 0.7360 (t80) REVERT: B 1063 TYR cc_start: 0.9042 (t80) cc_final: 0.8544 (t80) REVERT: B 1067 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7538 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8416 (tt) cc_final: 0.8088 (tt) REVERT: B 1134 LEU cc_start: 0.8769 (mt) cc_final: 0.8540 (mm) REVERT: B 1149 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8143 (tttt) REVERT: C 144 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6583 (ptm-80) REVERT: C 410 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: C 711 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7518 (ptm-80) REVERT: C 770 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6799 (ttp80) REVERT: C 972 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9005 (mp) REVERT: C 1015 TYR cc_start: 0.8081 (t80) cc_final: 0.7339 (t80) REVERT: C 1042 MET cc_start: 0.8731 (mtp) cc_final: 0.8385 (mtm) REVERT: C 1063 TYR cc_start: 0.9052 (t80) cc_final: 0.8621 (t80) REVERT: C 1067 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7480 (ptm-80) REVERT: C 1118 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 1154 LYS cc_start: 0.8172 (mttt) cc_final: 0.7968 (mtpt) REVERT: D 144 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6588 (ptm-80) REVERT: D 355 MET cc_start: 0.4884 (tpp) cc_final: 0.4595 (mmm) REVERT: D 410 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: D 430 MET cc_start: 0.7581 (tmm) cc_final: 0.7296 (mmm) REVERT: D 611 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7116 (mtm110) REVERT: D 770 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6811 (ttp80) REVERT: D 972 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 1015 TYR cc_start: 0.8079 (t80) cc_final: 0.7340 (t80) REVERT: D 1063 TYR cc_start: 0.9031 (t80) cc_final: 0.8596 (t80) REVERT: D 1067 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7484 (ptm-80) REVERT: D 1068 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7832 (tm-30) outliers start: 157 outliers final: 55 residues processed: 648 average time/residue: 0.4215 time to fit residues: 427.2946 Evaluate side-chains 563 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 496 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1166 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 267 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C 260 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS D 260 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 GLN D1128 HIS D1161 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30392 Z= 0.296 Angle : 0.707 9.975 41236 Z= 0.335 Chirality : 0.042 0.245 4660 Planarity : 0.005 0.066 5152 Dihedral : 7.487 59.948 4932 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.21 % Allowed : 16.74 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3640 helix: 0.30 (0.10), residues: 2388 sheet: -3.37 (0.37), residues: 152 loop : -2.79 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 152 HIS 0.005 0.001 HIS B 908 PHE 0.020 0.002 PHE B 627 TYR 0.029 0.001 TYR D 103 ARG 0.008 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 524 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.2891 (mmt-90) cc_final: 0.2640 (mmm-85) REVERT: A 405 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6777 (tpt90) REVERT: A 410 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: A 430 MET cc_start: 0.7603 (tmm) cc_final: 0.6962 (tpt) REVERT: A 570 ASN cc_start: 0.8676 (t0) cc_final: 0.8423 (t0) REVERT: A 588 SER cc_start: 0.8992 (m) cc_final: 0.8728 (m) REVERT: A 611 ARG cc_start: 0.7718 (mtm180) cc_final: 0.6982 (mtm110) REVERT: A 770 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6838 (ttp80) REVERT: A 1015 TYR cc_start: 0.8256 (t80) cc_final: 0.7393 (t80) REVERT: A 1063 TYR cc_start: 0.9100 (t80) cc_final: 0.8585 (t80) REVERT: A 1067 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7490 (ptm-80) REVERT: A 1128 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7833 (m-70) REVERT: A 1154 LYS cc_start: 0.8204 (mttt) cc_final: 0.7973 (mtpt) REVERT: B 410 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: B 578 PHE cc_start: 0.9307 (m-10) cc_final: 0.9062 (m-80) REVERT: B 770 ARG cc_start: 0.7507 (mtp85) cc_final: 0.6822 (ttp80) REVERT: B 827 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7280 (tp30) REVERT: B 1015 TYR cc_start: 0.8247 (t80) cc_final: 0.7312 (t80) REVERT: B 1067 ARG cc_start: 0.8146 (ptm-80) cc_final: 0.7643 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8461 (tt) cc_final: 0.8130 (tt) REVERT: B 1128 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: B 1134 LEU cc_start: 0.8807 (mt) cc_final: 0.8570 (mm) REVERT: B 1149 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8124 (tttt) REVERT: C 334 ARG cc_start: 0.2888 (mmt-90) cc_final: 0.2636 (mmm-85) REVERT: C 410 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: C 581 MET cc_start: 0.8263 (mmt) cc_final: 0.7933 (tpp) REVERT: C 770 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6824 (ttp80) REVERT: C 1015 TYR cc_start: 0.8247 (t80) cc_final: 0.7279 (t80) REVERT: C 1042 MET cc_start: 0.8783 (mtp) cc_final: 0.8576 (mtm) REVERT: C 1045 TYR cc_start: 0.8700 (t80) cc_final: 0.8490 (t80) REVERT: C 1063 TYR cc_start: 0.9101 (t80) cc_final: 0.8586 (t80) REVERT: C 1067 ARG cc_start: 0.8092 (ptm-80) cc_final: 0.7491 (ptm-80) REVERT: C 1128 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.7657 (m90) REVERT: C 1154 LYS cc_start: 0.8215 (mttt) cc_final: 0.7871 (mtpt) REVERT: D 252 ARG cc_start: 0.5138 (tmm-80) cc_final: 0.4794 (mmm-85) REVERT: D 355 MET cc_start: 0.4695 (tpp) cc_final: 0.4309 (mmm) REVERT: D 410 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7098 (mp10) REVERT: D 430 MET cc_start: 0.7691 (tmm) cc_final: 0.7452 (mmm) REVERT: D 581 MET cc_start: 0.8270 (mmt) cc_final: 0.7942 (tpp) REVERT: D 611 ARG cc_start: 0.7818 (mtm180) cc_final: 0.7245 (mtm110) REVERT: D 770 ARG cc_start: 0.7525 (mtp85) cc_final: 0.6832 (ttp80) REVERT: D 827 GLU cc_start: 0.7409 (tp30) cc_final: 0.7106 (tp30) REVERT: D 1015 TYR cc_start: 0.8246 (t80) cc_final: 0.7308 (t80) REVERT: D 1063 TYR cc_start: 0.9091 (t80) cc_final: 0.8574 (t80) REVERT: D 1067 ARG cc_start: 0.8093 (ptm-80) cc_final: 0.7479 (ptm-80) REVERT: D 1118 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 159 outliers final: 108 residues processed: 629 average time/residue: 0.4228 time to fit residues: 415.0185 Evaluate side-chains 611 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 495 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1128 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1128 HIS Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1166 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 359 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 188 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 505 HIS ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN B 505 HIS ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1161 GLN C 260 GLN C 419 GLN C 505 HIS ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS D 260 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30392 Z= 0.210 Angle : 0.647 10.570 41236 Z= 0.307 Chirality : 0.040 0.225 4660 Planarity : 0.005 0.062 5152 Dihedral : 6.958 59.970 4932 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.62 % Allowed : 18.05 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3640 helix: 0.65 (0.11), residues: 2412 sheet: -2.96 (0.40), residues: 144 loop : -2.64 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 152 HIS 0.010 0.001 HIS C1128 PHE 0.019 0.001 PHE C 578 TYR 0.019 0.001 TYR A 103 ARG 0.006 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 508 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8504 (tp) cc_final: 0.8303 (tp) REVERT: A 334 ARG cc_start: 0.2899 (mmt-90) cc_final: 0.2507 (mmm-85) REVERT: A 410 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: A 588 SER cc_start: 0.8975 (m) cc_final: 0.8725 (m) REVERT: A 611 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7148 (mtm110) REVERT: A 629 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 770 ARG cc_start: 0.7498 (mtp85) cc_final: 0.6816 (ttp80) REVERT: A 830 ARG cc_start: 0.7516 (tmm-80) cc_final: 0.7093 (tmm-80) REVERT: A 972 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9024 (mp) REVERT: A 1015 TYR cc_start: 0.8164 (t80) cc_final: 0.7435 (t80) REVERT: A 1042 MET cc_start: 0.8689 (mtp) cc_final: 0.8415 (mtm) REVERT: A 1063 TYR cc_start: 0.9037 (t80) cc_final: 0.8504 (t80) REVERT: A 1067 ARG cc_start: 0.8030 (ptm-80) cc_final: 0.7425 (ptm-80) REVERT: A 1154 LYS cc_start: 0.8250 (mttt) cc_final: 0.7973 (mtpt) REVERT: A 1166 ARG cc_start: 0.7582 (tpt-90) cc_final: 0.7132 (ttt90) REVERT: B 410 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: B 576 MET cc_start: 0.7939 (mmm) cc_final: 0.7632 (tpt) REVERT: B 640 ARG cc_start: 0.8471 (mtp180) cc_final: 0.8070 (mtp180) REVERT: B 770 ARG cc_start: 0.7488 (mtp85) cc_final: 0.6801 (ttp80) REVERT: B 1015 TYR cc_start: 0.8098 (t80) cc_final: 0.7521 (t80) REVERT: B 1042 MET cc_start: 0.8720 (mtp) cc_final: 0.8393 (mtm) REVERT: B 1063 TYR cc_start: 0.9067 (t80) cc_final: 0.8588 (t80) REVERT: B 1067 ARG cc_start: 0.8056 (ptm-80) cc_final: 0.7466 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8419 (tt) cc_final: 0.8087 (tt) REVERT: B 1136 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7699 (mtm110) REVERT: B 1149 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8130 (tttt) REVERT: C 334 ARG cc_start: 0.2741 (mmt-90) cc_final: 0.2478 (mmm-85) REVERT: C 410 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: C 629 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7355 (mm-30) REVERT: C 770 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6780 (ttp80) REVERT: C 830 ARG cc_start: 0.7518 (tmm-80) cc_final: 0.7099 (tmm-80) REVERT: C 1015 TYR cc_start: 0.8102 (t80) cc_final: 0.7590 (t80) REVERT: C 1042 MET cc_start: 0.8766 (mtp) cc_final: 0.8405 (mtm) REVERT: C 1063 TYR cc_start: 0.9040 (t80) cc_final: 0.8503 (t80) REVERT: C 1067 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7421 (ptm-80) REVERT: D 355 MET cc_start: 0.4705 (tpp) cc_final: 0.4392 (mmm) REVERT: D 410 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: D 578 PHE cc_start: 0.9226 (m-80) cc_final: 0.8963 (m-80) REVERT: D 599 MET cc_start: 0.8118 (ptp) cc_final: 0.7909 (ptp) REVERT: D 611 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7393 (mtm110) REVERT: D 629 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7311 (mm-30) REVERT: D 770 ARG cc_start: 0.7503 (mtp85) cc_final: 0.6790 (ttp80) REVERT: D 830 ARG cc_start: 0.7545 (tmm-80) cc_final: 0.7155 (tmm-80) REVERT: D 1015 TYR cc_start: 0.8092 (t80) cc_final: 0.7586 (t80) REVERT: D 1063 TYR cc_start: 0.9036 (t80) cc_final: 0.8512 (t80) REVERT: D 1067 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7447 (ptm-80) REVERT: D 1118 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8423 (tm-30) REVERT: D 1156 ASP cc_start: 0.8189 (m-30) cc_final: 0.7889 (m-30) outliers start: 141 outliers final: 88 residues processed: 598 average time/residue: 0.4319 time to fit residues: 402.5805 Evaluate side-chains 574 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 481 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1054 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 0.0070 chunk 302 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1161 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS C1161 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30392 Z= 0.260 Angle : 0.670 13.225 41236 Z= 0.318 Chirality : 0.041 0.200 4660 Planarity : 0.005 0.062 5152 Dihedral : 6.911 59.767 4928 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.46 % Allowed : 18.55 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3640 helix: 0.71 (0.11), residues: 2412 sheet: -2.71 (0.42), residues: 144 loop : -2.59 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 691 HIS 0.004 0.001 HIS B 908 PHE 0.022 0.002 PHE C 578 TYR 0.019 0.001 TYR D 103 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 504 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7424 (ptm-80) cc_final: 0.7020 (ptm-80) REVERT: A 410 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: A 465 SER cc_start: 0.9211 (t) cc_final: 0.8954 (p) REVERT: A 570 ASN cc_start: 0.8665 (t0) cc_final: 0.8448 (t0) REVERT: A 588 SER cc_start: 0.8977 (m) cc_final: 0.8723 (m) REVERT: A 611 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7123 (mtm110) REVERT: A 629 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 635 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7531 (mp0) REVERT: A 770 ARG cc_start: 0.7517 (mtp85) cc_final: 0.6791 (ttp80) REVERT: A 1015 TYR cc_start: 0.8238 (t80) cc_final: 0.7441 (t80) REVERT: A 1063 TYR cc_start: 0.9050 (t80) cc_final: 0.8568 (t80) REVERT: A 1067 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7458 (ptm-80) REVERT: A 1128 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7894 (m-70) REVERT: A 1154 LYS cc_start: 0.8199 (mttt) cc_final: 0.7965 (mtpt) REVERT: B 410 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: B 570 ASN cc_start: 0.8704 (t0) cc_final: 0.8481 (t0) REVERT: B 578 PHE cc_start: 0.9281 (m-80) cc_final: 0.8996 (m-80) REVERT: B 770 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6805 (ttp80) REVERT: B 1015 TYR cc_start: 0.8199 (t80) cc_final: 0.7334 (t80) REVERT: B 1042 MET cc_start: 0.8777 (mtp) cc_final: 0.8445 (mtm) REVERT: B 1063 TYR cc_start: 0.9064 (t80) cc_final: 0.8577 (t80) REVERT: B 1067 ARG cc_start: 0.8069 (ptm-80) cc_final: 0.7478 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8485 (tt) cc_final: 0.8174 (tt) REVERT: B 1128 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7893 (m-70) REVERT: B 1136 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7713 (mtm110) REVERT: B 1149 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8100 (tttt) REVERT: C 254 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7305 (mt-10) REVERT: C 410 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: C 465 SER cc_start: 0.9195 (t) cc_final: 0.8930 (p) REVERT: C 581 MET cc_start: 0.8237 (mmt) cc_final: 0.7953 (tpp) REVERT: C 629 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7374 (mm-30) REVERT: C 635 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7524 (mp0) REVERT: C 770 ARG cc_start: 0.7494 (mtp85) cc_final: 0.6788 (ttp80) REVERT: C 1015 TYR cc_start: 0.8202 (t80) cc_final: 0.7347 (t80) REVERT: C 1042 MET cc_start: 0.8773 (mtp) cc_final: 0.8455 (mtm) REVERT: C 1063 TYR cc_start: 0.9051 (t80) cc_final: 0.8567 (t80) REVERT: C 1067 ARG cc_start: 0.8050 (ptm-80) cc_final: 0.7456 (ptm-80) REVERT: C 1154 LYS cc_start: 0.8080 (mttt) cc_final: 0.7849 (mtpt) REVERT: D 355 MET cc_start: 0.4741 (tpp) cc_final: 0.4488 (mmm) REVERT: D 410 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: D 611 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7448 (mtm110) REVERT: D 635 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7539 (mp0) REVERT: D 770 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6798 (ttp80) REVERT: D 1015 TYR cc_start: 0.8195 (t80) cc_final: 0.7347 (t80) REVERT: D 1063 TYR cc_start: 0.9052 (t80) cc_final: 0.8572 (t80) REVERT: D 1067 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7439 (ptm-80) REVERT: D 1156 ASP cc_start: 0.8191 (m-30) cc_final: 0.7871 (m-30) outliers start: 136 outliers final: 102 residues processed: 591 average time/residue: 0.4263 time to fit residues: 395.4848 Evaluate side-chains 598 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 490 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1128 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1143 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.1980 chunk 143 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 244 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 GLN C 260 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS D 419 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30392 Z= 0.190 Angle : 0.664 13.965 41236 Z= 0.308 Chirality : 0.042 0.370 4660 Planarity : 0.004 0.059 5152 Dihedral : 6.595 57.476 4928 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.06 % Allowed : 19.00 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3640 helix: 0.88 (0.11), residues: 2416 sheet: -2.59 (0.43), residues: 144 loop : -2.46 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 691 HIS 0.006 0.001 HIS B 447 PHE 0.029 0.001 PHE A 578 TYR 0.015 0.001 TYR D 103 ARG 0.006 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 499 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ARG cc_start: 0.7645 (tpt-90) cc_final: 0.7278 (tpp-160) REVERT: A 410 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: A 588 SER cc_start: 0.8941 (m) cc_final: 0.8687 (m) REVERT: A 611 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7302 (mtm110) REVERT: A 629 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 770 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6793 (ttp80) REVERT: A 972 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9013 (mp) REVERT: A 1015 TYR cc_start: 0.8170 (t80) cc_final: 0.7445 (t80) REVERT: A 1032 ASN cc_start: 0.8859 (m110) cc_final: 0.8650 (m110) REVERT: A 1063 TYR cc_start: 0.9035 (t80) cc_final: 0.8590 (t80) REVERT: A 1067 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7415 (ptm-80) REVERT: A 1154 LYS cc_start: 0.8196 (mttt) cc_final: 0.7974 (mtpt) REVERT: B 410 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: B 433 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7967 (mp) REVERT: B 570 ASN cc_start: 0.8663 (t0) cc_final: 0.8446 (t0) REVERT: B 770 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6780 (ttp80) REVERT: B 1015 TYR cc_start: 0.8085 (t80) cc_final: 0.7539 (t80) REVERT: B 1042 MET cc_start: 0.8671 (mtp) cc_final: 0.8326 (mtm) REVERT: B 1063 TYR cc_start: 0.9033 (t80) cc_final: 0.8571 (t80) REVERT: B 1067 ARG cc_start: 0.8039 (ptm-80) cc_final: 0.7433 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8451 (tt) cc_final: 0.8106 (tt) REVERT: B 1128 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7738 (m-70) REVERT: B 1136 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7736 (mtm110) REVERT: B 1149 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8127 (tttt) REVERT: C 254 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 410 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: C 629 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 635 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7507 (mp0) REVERT: C 770 ARG cc_start: 0.7471 (mtp85) cc_final: 0.6770 (ttp80) REVERT: C 830 ARG cc_start: 0.7418 (tmm-80) cc_final: 0.7086 (tmm-80) REVERT: C 1015 TYR cc_start: 0.8104 (t80) cc_final: 0.7265 (t80) REVERT: C 1032 ASN cc_start: 0.8875 (m110) cc_final: 0.8634 (m110) REVERT: C 1042 MET cc_start: 0.8769 (mtp) cc_final: 0.8415 (mtm) REVERT: C 1063 TYR cc_start: 0.9028 (t80) cc_final: 0.8511 (t80) REVERT: C 1067 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7412 (ptm-80) REVERT: C 1154 LYS cc_start: 0.8024 (mttt) cc_final: 0.7800 (mtpt) REVERT: D 405 ARG cc_start: 0.7622 (tpt-90) cc_final: 0.7364 (tpp-160) REVERT: D 410 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: D 599 MET cc_start: 0.8099 (ptp) cc_final: 0.7893 (ptp) REVERT: D 629 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7354 (mm-30) REVERT: D 770 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6795 (ttp80) REVERT: D 1015 TYR cc_start: 0.8067 (t80) cc_final: 0.7545 (t80) REVERT: D 1063 TYR cc_start: 0.9032 (t80) cc_final: 0.8589 (t80) REVERT: D 1067 ARG cc_start: 0.8000 (ptm-80) cc_final: 0.7463 (ptm-80) REVERT: D 1156 ASP cc_start: 0.8142 (m-30) cc_final: 0.7790 (m-30) outliers start: 124 outliers final: 97 residues processed: 579 average time/residue: 0.4201 time to fit residues: 383.7780 Evaluate side-chains 590 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 486 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1143 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 334 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 332 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS D 505 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30392 Z= 0.271 Angle : 0.710 13.916 41236 Z= 0.329 Chirality : 0.043 0.335 4660 Planarity : 0.005 0.062 5152 Dihedral : 6.771 57.674 4928 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.83 % Allowed : 19.27 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3640 helix: 0.79 (0.11), residues: 2416 sheet: -2.45 (0.44), residues: 144 loop : -2.49 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 691 HIS 0.005 0.001 HIS C 908 PHE 0.029 0.002 PHE A 578 TYR 0.017 0.001 TYR D 103 ARG 0.008 0.000 ARG C 611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 497 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: A 570 ASN cc_start: 0.8663 (t0) cc_final: 0.8343 (t0) REVERT: A 588 SER cc_start: 0.8965 (m) cc_final: 0.8707 (m) REVERT: A 611 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7077 (mtm110) REVERT: A 635 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 770 ARG cc_start: 0.7521 (mtp85) cc_final: 0.6811 (ttp80) REVERT: A 830 ARG cc_start: 0.7375 (tmm-80) cc_final: 0.7054 (tmm-80) REVERT: A 1015 TYR cc_start: 0.8370 (t80) cc_final: 0.7563 (t80) REVERT: A 1063 TYR cc_start: 0.9061 (t80) cc_final: 0.8570 (t80) REVERT: A 1067 ARG cc_start: 0.8050 (ptm-80) cc_final: 0.7415 (ptm-80) REVERT: A 1128 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7962 (m-70) REVERT: A 1154 LYS cc_start: 0.8215 (mttt) cc_final: 0.7984 (mtpt) REVERT: B 410 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: B 433 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8005 (mp) REVERT: B 578 PHE cc_start: 0.9287 (m-80) cc_final: 0.8851 (m-80) REVERT: B 770 ARG cc_start: 0.7511 (mtp85) cc_final: 0.6794 (ttp80) REVERT: B 1015 TYR cc_start: 0.8177 (t80) cc_final: 0.7463 (t80) REVERT: B 1063 TYR cc_start: 0.9033 (t80) cc_final: 0.8554 (t80) REVERT: B 1067 ARG cc_start: 0.8066 (ptm-80) cc_final: 0.7463 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8488 (tt) cc_final: 0.8138 (tt) REVERT: B 1128 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7948 (m-70) REVERT: B 1149 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8091 (tttt) REVERT: C 403 TRP cc_start: 0.8897 (m-10) cc_final: 0.8681 (m-10) REVERT: C 410 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: C 581 MET cc_start: 0.8254 (mmt) cc_final: 0.7986 (tpp) REVERT: C 635 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7499 (mp0) REVERT: C 770 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6786 (ttp80) REVERT: C 1015 TYR cc_start: 0.8242 (t80) cc_final: 0.7441 (t80) REVERT: C 1042 MET cc_start: 0.8772 (mtp) cc_final: 0.8543 (mtm) REVERT: C 1063 TYR cc_start: 0.9045 (t80) cc_final: 0.8592 (t80) REVERT: C 1067 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.7447 (ptm-80) REVERT: C 1154 LYS cc_start: 0.8067 (mttt) cc_final: 0.7865 (mtpt) REVERT: D 403 TRP cc_start: 0.8938 (m-10) cc_final: 0.8646 (m-10) REVERT: D 410 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: D 429 LEU cc_start: 0.8171 (tp) cc_final: 0.7895 (tp) REVERT: D 770 ARG cc_start: 0.7526 (mtp85) cc_final: 0.6814 (ttp80) REVERT: D 830 ARG cc_start: 0.7377 (tmm-80) cc_final: 0.7065 (tmm-80) REVERT: D 1015 TYR cc_start: 0.8193 (t80) cc_final: 0.7362 (t80) REVERT: D 1063 TYR cc_start: 0.9064 (t80) cc_final: 0.8574 (t80) REVERT: D 1067 ARG cc_start: 0.8024 (ptm-80) cc_final: 0.7412 (ptm-80) REVERT: D 1156 ASP cc_start: 0.8218 (m-30) cc_final: 0.7948 (m-30) outliers start: 117 outliers final: 103 residues processed: 572 average time/residue: 0.4211 time to fit residues: 379.4844 Evaluate side-chains 590 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 480 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1128 HIS Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.9980 chunk 353 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 370 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN B1161 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30392 Z= 0.200 Angle : 0.677 13.781 41236 Z= 0.313 Chirality : 0.042 0.323 4660 Planarity : 0.004 0.060 5152 Dihedral : 6.508 55.238 4928 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.70 % Allowed : 19.53 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3640 helix: 0.93 (0.11), residues: 2412 sheet: -2.46 (0.43), residues: 144 loop : -2.39 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 691 HIS 0.002 0.001 HIS C 908 PHE 0.028 0.001 PHE A 578 TYR 0.021 0.001 TYR A 103 ARG 0.007 0.000 ARG C 611 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 488 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 TRP cc_start: 0.8928 (m-10) cc_final: 0.8699 (m-10) REVERT: A 410 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: A 588 SER cc_start: 0.8963 (m) cc_final: 0.8700 (m) REVERT: A 611 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7366 (mtm110) REVERT: A 629 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 770 ARG cc_start: 0.7496 (mtp85) cc_final: 0.6792 (ttp80) REVERT: A 830 ARG cc_start: 0.7371 (tmm-80) cc_final: 0.7107 (ttt-90) REVERT: A 1015 TYR cc_start: 0.8259 (t80) cc_final: 0.7487 (t80) REVERT: A 1063 TYR cc_start: 0.9018 (t80) cc_final: 0.8603 (t80) REVERT: A 1067 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7426 (ptm-80) REVERT: A 1154 LYS cc_start: 0.8226 (mttt) cc_final: 0.7834 (mtpt) REVERT: B 410 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: B 433 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (mp) REVERT: B 578 PHE cc_start: 0.9226 (m-80) cc_final: 0.8974 (m-80) REVERT: B 770 ARG cc_start: 0.7496 (mtp85) cc_final: 0.6770 (ttp80) REVERT: B 1015 TYR cc_start: 0.8074 (t80) cc_final: 0.7474 (t80) REVERT: B 1042 MET cc_start: 0.8671 (mtp) cc_final: 0.8360 (mtm) REVERT: B 1063 TYR cc_start: 0.9018 (t80) cc_final: 0.8575 (t80) REVERT: B 1067 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7444 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8432 (tt) cc_final: 0.8082 (tt) REVERT: B 1128 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.7803 (m-70) REVERT: B 1149 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8133 (tttt) REVERT: C 410 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: C 629 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 770 ARG cc_start: 0.7482 (mtp85) cc_final: 0.6775 (ttp80) REVERT: C 830 ARG cc_start: 0.7387 (tmm-80) cc_final: 0.7146 (ttt-90) REVERT: C 1015 TYR cc_start: 0.8176 (t80) cc_final: 0.7418 (t80) REVERT: C 1032 ASN cc_start: 0.8876 (m110) cc_final: 0.8652 (m110) REVERT: C 1042 MET cc_start: 0.8790 (mtp) cc_final: 0.8440 (mtm) REVERT: C 1063 TYR cc_start: 0.9028 (t80) cc_final: 0.8600 (t80) REVERT: C 1067 ARG cc_start: 0.8024 (ptm-80) cc_final: 0.7437 (ptm-80) REVERT: C 1156 ASP cc_start: 0.8370 (m-30) cc_final: 0.8143 (m-30) REVERT: D 403 TRP cc_start: 0.8927 (m-10) cc_final: 0.8651 (m-10) REVERT: D 410 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: D 429 LEU cc_start: 0.8147 (tp) cc_final: 0.7800 (tp) REVERT: D 599 MET cc_start: 0.8131 (ptp) cc_final: 0.7904 (ptp) REVERT: D 629 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 770 ARG cc_start: 0.7492 (mtp85) cc_final: 0.6793 (ttp80) REVERT: D 830 ARG cc_start: 0.7388 (tmm-80) cc_final: 0.7048 (tmm-80) REVERT: D 1015 TYR cc_start: 0.8077 (t80) cc_final: 0.7568 (t80) REVERT: D 1063 TYR cc_start: 0.9021 (t80) cc_final: 0.8605 (t80) REVERT: D 1067 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7407 (ptm-80) REVERT: D 1154 LYS cc_start: 0.8106 (mttt) cc_final: 0.7802 (mtpt) outliers start: 113 outliers final: 97 residues processed: 565 average time/residue: 0.4198 time to fit residues: 371.3686 Evaluate side-chains 579 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 476 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1068 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 573 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS D 293 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.207196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128899 restraints weight = 34513.484| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.23 r_work: 0.3080 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30392 Z= 0.292 Angle : 0.722 13.643 41236 Z= 0.336 Chirality : 0.044 0.315 4660 Planarity : 0.005 0.063 5152 Dihedral : 6.803 59.524 4928 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.93 % Allowed : 19.40 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3640 helix: 0.78 (0.11), residues: 2416 sheet: -2.76 (0.36), residues: 192 loop : -2.38 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 691 HIS 0.006 0.001 HIS A 908 PHE 0.029 0.002 PHE A 578 TYR 0.017 0.001 TYR D 103 ARG 0.012 0.000 ARG C 611 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8335.45 seconds wall clock time: 148 minutes 50.66 seconds (8930.66 seconds total)