Starting phenix.real_space_refine on Tue Mar 12 03:58:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/03_2024/6k32_9907_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 2.237 sd= 16.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 2 5.21 5 S 242 5.16 5 C 38758 2.51 5 N 10636 2.21 5 O 11711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A ARG 950": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "A ARG 1175": "NH1" <-> "NH2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 1116": "NH1" <-> "NH2" Residue "C ARG 1255": "NH1" <-> "NH2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 1003": "NH1" <-> "NH2" Residue "D ARG 1116": "NH1" <-> "NH2" Residue "D ARG 1255": "NH1" <-> "NH2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1116": "NH1" <-> "NH2" Residue "E ARG 1255": "NH1" <-> "NH2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F ARG 1116": "NH1" <-> "NH2" Residue "F ARG 1255": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "G TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1116": "NH1" <-> "NH2" Residue "G ARG 1255": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61364 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9652 Classifications: {'peptide': 1208} Link IDs: {'CIS': 8, 'PTRANS': 37, 'TRANS': 1162} Chain: "B" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3981 Classifications: {'peptide': 498} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 475} Chain breaks: 2 Chain: "t" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "p" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'3PO': 1} Inner-chain residues flagged as termini: ['pdbres=" A p 2 "'] Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="3PO p 1 " pdbres=" A p 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 9622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9622 Classifications: {'peptide': 1220} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 59, 'TRANS': 1152} Chain: "D" Number of atoms: 9447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9447 Classifications: {'peptide': 1197} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 59, 'TRANS': 1133} Chain breaks: 1 Chain: "E" Number of atoms: 9402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9402 Classifications: {'peptide': 1191} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 58, 'TRANS': 1129} Chain breaks: 1 Chain: "F" Number of atoms: 9402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9402 Classifications: {'peptide': 1191} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 58, 'TRANS': 1129} Chain breaks: 1 Chain: "G" Number of atoms: 9618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9618 Classifications: {'peptide': 1218} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 61, 'TRANS': 1152} Chain breaks: 1 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {' MG': 2, 'DPO': 1, 'MG7%rna3p': 1, 'UTP': 1} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 23.88, per 1000 atoms: 0.39 Number of scatterers: 61364 At special positions: 0 Unit cell: (262.89, 281.94, 217.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 242 16.00 P 15 15.00 Mg 2 11.99 O 11711 8.00 N 10636 7.00 C 38758 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 Atom "HETATM13744 O3B 3PO p 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM13744 O3B 3PO p 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.64 Conformation dependent library (CDL) restraints added in 8.9 seconds 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 69 sheets defined 33.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.33 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.757A pdb=" N ALA A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 129 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS A 134 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.661A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 203 through 219 removed outlier: 4.380A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.636A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.754A pdb=" N LYS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 4.102A pdb=" N LEU A 261 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.664A pdb=" N SER A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.506A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.912A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.611A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.783A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.780A pdb=" N SER A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.918A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 557 through 573 removed outlier: 4.111A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 647 through 666 removed outlier: 3.763A pdb=" N LEU A 651 " --> pdb=" O HIS A 647 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 706 removed outlier: 4.030A pdb=" N SER A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 755 through 767 removed outlier: 3.702A pdb=" N LEU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 786 removed outlier: 3.589A pdb=" N PHE A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 removed outlier: 3.648A pdb=" N ASP A 802 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 871 through 877 removed outlier: 3.907A pdb=" N LEU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 887 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.654A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 923 removed outlier: 3.502A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 937 Processing helix chain 'A' and resid 947 through 959 Processing helix chain 'A' and resid 971 through 984 removed outlier: 4.212A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER A 980 " --> pdb=" O LYS A 976 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1006 removed outlier: 3.769A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1068 through 1076 removed outlier: 4.302A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.622A pdb=" N ILE A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1118 through 1132 removed outlier: 3.695A pdb=" N LEU A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1174 through 1188 removed outlier: 3.639A pdb=" N ASN A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A1186 " --> pdb=" O SER A1182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1187 " --> pdb=" O TYR A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.519A pdb=" N VAL A1210 " --> pdb=" O LEU A1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.520A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.764A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.815A pdb=" N MET B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.563A pdb=" N ALA B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 143 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.970A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.552A pdb=" N PHE B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.938A pdb=" N ALA B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.661A pdb=" N ALA B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.738A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 392' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.617A pdb=" N MET B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.725A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.871A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 456 " --> pdb=" O MET B 452 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 removed outlier: 3.754A pdb=" N SER B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 524 through 537 removed outlier: 4.058A pdb=" N LEU B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 removed outlier: 4.102A pdb=" N LYS B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 124 No H-bonds generated for 'chain 'C' and resid 121 through 124' Processing helix chain 'C' and resid 126 through 129 No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 184 through 187 No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 244 through 259 removed outlier: 4.283A pdb=" N VAL C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 308 through 318 removed outlier: 4.173A pdb=" N MET C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.777A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.629A pdb=" N ILE C 376 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 377 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 380 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.627A pdb=" N ILE C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.956A pdb=" N GLU C 423 " --> pdb=" O PRO C 420 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 427 " --> pdb=" O GLY C 424 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 431 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 435 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 471 removed outlier: 4.031A pdb=" N ALA C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 485 removed outlier: 4.038A pdb=" N ALA C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 520 removed outlier: 3.507A pdb=" N ILE C 508 " --> pdb=" O PRO C 505 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 509 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 510 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 515 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 516 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 517 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE C 520 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 529 through 543 removed outlier: 3.987A pdb=" N LEU C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 removed outlier: 3.538A pdb=" N GLY C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 554 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 598 through 604 Processing helix chain 'C' and resid 617 through 620 No H-bonds generated for 'chain 'C' and resid 617 through 620' Processing helix chain 'C' and resid 651 through 667 removed outlier: 3.729A pdb=" N THR C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 664 " --> pdb=" O ALA C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 684 removed outlier: 4.040A pdb=" N THR C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 683 " --> pdb=" O CYS C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 701 removed outlier: 3.822A pdb=" N ILE C 694 " --> pdb=" O GLN C 690 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 696 " --> pdb=" O ASP C 692 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 764 through 767 No H-bonds generated for 'chain 'C' and resid 764 through 767' Processing helix chain 'C' and resid 773 through 776 No H-bonds generated for 'chain 'C' and resid 773 through 776' Processing helix chain 'C' and resid 796 through 807 removed outlier: 4.279A pdb=" N LEU C 800 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER C 801 " --> pdb=" O THR C 798 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 802 " --> pdb=" O THR C 799 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 804 " --> pdb=" O SER C 801 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C 805 " --> pdb=" O GLN C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 removed outlier: 4.061A pdb=" N ILE C 820 " --> pdb=" O PRO C 816 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY C 826 " --> pdb=" O MET C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 3.814A pdb=" N SER C 857 " --> pdb=" O ASP C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.915A pdb=" N ILE C 865 " --> pdb=" O GLU C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 887 Processing helix chain 'C' and resid 904 through 912 removed outlier: 3.733A pdb=" N TYR C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 962 through 970 removed outlier: 3.582A pdb=" N GLN C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 removed outlier: 3.510A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1002 Processing helix chain 'C' and resid 1038 through 1040 No H-bonds generated for 'chain 'C' and resid 1038 through 1040' Processing helix chain 'C' and resid 1049 through 1062 removed outlier: 3.852A pdb=" N ARG C1053 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C1060 " --> pdb=" O SER C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1162 removed outlier: 3.546A pdb=" N ILE C1156 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1190 through 1194 Processing helix chain 'C' and resid 1325 through 1327 No H-bonds generated for 'chain 'C' and resid 1325 through 1327' Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'D' and resid 191 through 194 No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 244 through 259 removed outlier: 3.603A pdb=" N TYR D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 248 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 254 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 257 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 352 through 363 removed outlier: 3.599A pdb=" N VAL D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 382 removed outlier: 3.609A pdb=" N GLN D 380 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.648A pdb=" N ARG D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 437 removed outlier: 4.166A pdb=" N GLU D 423 " --> pdb=" O PRO D 420 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL D 427 " --> pdb=" O GLY D 424 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 429 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 431 " --> pdb=" O GLN D 428 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 435 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 removed outlier: 4.295A pdb=" N ARG D 461 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL D 463 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 464 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 466 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 468 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.652A pdb=" N HIS D 479 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL D 486 " --> pdb=" O ILE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 520 removed outlier: 3.810A pdb=" N VAL D 510 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 512 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 515 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 516 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 519 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 520 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 529 through 543 removed outlier: 4.489A pdb=" N LEU D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.530A pdb=" N GLY D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 588 through 590 No H-bonds generated for 'chain 'D' and resid 588 through 590' Processing helix chain 'D' and resid 600 through 604 Processing helix chain 'D' and resid 617 through 621 Processing helix chain 'D' and resid 649 through 669 removed outlier: 4.102A pdb=" N ASN D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 684 Processing helix chain 'D' and resid 686 through 701 removed outlier: 3.660A pdb=" N ILE D 694 " --> pdb=" O GLN D 690 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 696 " --> pdb=" O ASP D 692 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP D 700 " --> pdb=" O VAL D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 709 Processing helix chain 'D' and resid 760 through 767 removed outlier: 3.878A pdb=" N VAL D 763 " --> pdb=" O THR D 760 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP D 764 " --> pdb=" O SER D 761 " (cutoff:3.500A) Proline residue: D 765 - end of helix No H-bonds generated for 'chain 'D' and resid 760 through 767' Processing helix chain 'D' and resid 797 through 807 removed outlier: 3.571A pdb=" N SER D 803 " --> pdb=" O THR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 823 removed outlier: 3.545A pdb=" N ASN D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET D 822 " --> pdb=" O ALA D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 858 removed outlier: 3.693A pdb=" N HIS D 858 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 904 through 909 removed outlier: 3.587A pdb=" N TYR D 909 " --> pdb=" O SER D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 951 No H-bonds generated for 'chain 'D' and resid 948 through 951' Processing helix chain 'D' and resid 962 through 970 removed outlier: 3.749A pdb=" N GLN D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 989 removed outlier: 3.709A pdb=" N GLN D 988 " --> pdb=" O GLU D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1004 Processing helix chain 'D' and resid 1038 through 1040 No H-bonds generated for 'chain 'D' and resid 1038 through 1040' Processing helix chain 'D' and resid 1049 through 1062 removed outlier: 4.066A pdb=" N ARG D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D1060 " --> pdb=" O SER D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1149 through 1162 removed outlier: 3.689A pdb=" N ILE D1156 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1190 through 1194 removed outlier: 3.537A pdb=" N MET D1194 " --> pdb=" O ALA D1190 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1190 through 1194' Processing helix chain 'E' and resid 184 through 187 No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 191 through 194 No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 244 through 259 removed outlier: 3.617A pdb=" N TYR E 247 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 248 " --> pdb=" O ALA E 245 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 254 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 256 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 258 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET E 259 " --> pdb=" O PHE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.540A pdb=" N LEU E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.816A pdb=" N MET E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 363 removed outlier: 3.509A pdb=" N VAL E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 395 through 397 No H-bonds generated for 'chain 'E' and resid 395 through 397' Processing helix chain 'E' and resid 405 through 418 removed outlier: 3.804A pdb=" N ARG E 410 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 437 removed outlier: 3.928A pdb=" N GLU E 423 " --> pdb=" O PRO E 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL E 427 " --> pdb=" O GLY E 424 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 431 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E 435 " --> pdb=" O GLY E 432 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 436 " --> pdb=" O TYR E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 469 removed outlier: 3.969A pdb=" N ALA E 465 " --> pdb=" O ARG E 461 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA E 468 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 486 removed outlier: 3.822A pdb=" N GLU E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL E 486 " --> pdb=" O ILE E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 removed outlier: 3.568A pdb=" N ILE E 508 " --> pdb=" O PRO E 505 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 509 " --> pdb=" O SER E 506 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 510 " --> pdb=" O SER E 507 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 515 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 516 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 517 " --> pdb=" O PHE E 514 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 519 " --> pdb=" O LEU E 516 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE E 520 " --> pdb=" O PHE E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 529 through 543 removed outlier: 3.532A pdb=" N ASN E 534 " --> pdb=" O GLY E 530 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 535 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 538 " --> pdb=" O ASN E 534 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 542 " --> pdb=" O LEU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.717A pdb=" N GLY E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 550 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 554 " --> pdb=" O ILE E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 587 through 589 No H-bonds generated for 'chain 'E' and resid 587 through 589' Processing helix chain 'E' and resid 598 through 607 removed outlier: 4.468A pdb=" N LEU E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE E 607 " --> pdb=" O ILE E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 621 Processing helix chain 'E' and resid 649 through 669 removed outlier: 3.630A pdb=" N THR E 658 " --> pdb=" O THR E 654 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN E 661 " --> pdb=" O ALA E 657 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 665 " --> pdb=" O ASN E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 684 removed outlier: 3.699A pdb=" N THR E 680 " --> pdb=" O THR E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 709 removed outlier: 3.876A pdb=" N ILE E 694 " --> pdb=" O GLN E 690 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL E 696 " --> pdb=" O ASP E 692 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER E 703 " --> pdb=" O THR E 699 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL E 704 " --> pdb=" O ASP E 700 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 705 " --> pdb=" O HIS E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 767 removed outlier: 3.686A pdb=" N VAL E 763 " --> pdb=" O THR E 760 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP E 764 " --> pdb=" O SER E 761 " (cutoff:3.500A) Proline residue: E 765 - end of helix No H-bonds generated for 'chain 'E' and resid 760 through 767' Processing helix chain 'E' and resid 797 through 809 removed outlier: 3.750A pdb=" N GLN E 802 " --> pdb=" O THR E 798 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 823 removed outlier: 4.129A pdb=" N ILE E 820 " --> pdb=" O PRO E 816 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN E 821 " --> pdb=" O ASP E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 858 Processing helix chain 'E' and resid 860 through 862 No H-bonds generated for 'chain 'E' and resid 860 through 862' Processing helix chain 'E' and resid 880 through 889 Processing helix chain 'E' and resid 904 through 912 removed outlier: 4.014A pdb=" N TYR E 909 " --> pdb=" O SER E 905 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 912 " --> pdb=" O THR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 928 No H-bonds generated for 'chain 'E' and resid 926 through 928' Processing helix chain 'E' and resid 948 through 950 No H-bonds generated for 'chain 'E' and resid 948 through 950' Processing helix chain 'E' and resid 962 through 970 removed outlier: 3.529A pdb=" N ALA E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 989 Processing helix chain 'E' and resid 998 through 1002 Processing helix chain 'E' and resid 1038 through 1040 No H-bonds generated for 'chain 'E' and resid 1038 through 1040' Processing helix chain 'E' and resid 1051 through 1062 removed outlier: 3.542A pdb=" N SER E1056 " --> pdb=" O LEU E1052 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E1057 " --> pdb=" O ARG E1053 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG E1060 " --> pdb=" O SER E1056 " (cutoff:3.500A) Processing helix chain 'E' and resid 1149 through 1162 removed outlier: 3.588A pdb=" N ILE E1156 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing helix chain 'E' and resid 1209 through 1211 No H-bonds generated for 'chain 'E' and resid 1209 through 1211' Processing helix chain 'E' and resid 1262 through 1265 Processing helix chain 'F' and resid 184 through 187 No H-bonds generated for 'chain 'F' and resid 184 through 187' Processing helix chain 'F' and resid 191 through 194 No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'F' and resid 244 through 259 removed outlier: 4.297A pdb=" N VAL F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 283 No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 352 through 366 removed outlier: 3.717A pdb=" N VAL F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F 362 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 382 removed outlier: 3.923A pdb=" N GLN F 380 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 381 " --> pdb=" O ALA F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 397 No H-bonds generated for 'chain 'F' and resid 395 through 397' Processing helix chain 'F' and resid 405 through 418 removed outlier: 3.719A pdb=" N ARG F 410 " --> pdb=" O ASP F 406 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 434 removed outlier: 3.898A pdb=" N GLU F 423 " --> pdb=" O PRO F 420 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 426 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL F 427 " --> pdb=" O GLY F 424 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 431 " --> pdb=" O GLN F 428 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 433 " --> pdb=" O ASN F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 4.466A pdb=" N ARG F 461 " --> pdb=" O SER F 458 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL F 463 " --> pdb=" O ALA F 460 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER F 464 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL F 466 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 467 " --> pdb=" O SER F 464 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 468 " --> pdb=" O ALA F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 483 removed outlier: 3.958A pdb=" N LEU F 480 " --> pdb=" O SER F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 520 removed outlier: 3.585A pdb=" N ILE F 508 " --> pdb=" O PRO F 505 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL F 509 " --> pdb=" O SER F 506 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL F 510 " --> pdb=" O SER F 507 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 516 " --> pdb=" O GLU F 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE F 517 " --> pdb=" O PHE F 514 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 519 " --> pdb=" O LEU F 516 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 520 " --> pdb=" O PHE F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 527 removed outlier: 3.566A pdb=" N ARG F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 543 removed outlier: 4.168A pdb=" N LEU F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 542 " --> pdb=" O LEU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 551 removed outlier: 4.155A pdb=" N GLY F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE F 550 " --> pdb=" O VAL F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 587 through 589 No H-bonds generated for 'chain 'F' and resid 587 through 589' Processing helix chain 'F' and resid 598 through 604 Processing helix chain 'F' and resid 617 through 620 No H-bonds generated for 'chain 'F' and resid 617 through 620' Processing helix chain 'F' and resid 649 through 669 removed outlier: 3.747A pdb=" N THR F 658 " --> pdb=" O THR F 654 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN F 661 " --> pdb=" O ALA F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 709 removed outlier: 3.998A pdb=" N THR F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 688 " --> pdb=" O LEU F 684 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 689 " --> pdb=" O ARG F 685 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 694 " --> pdb=" O GLN F 690 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL F 696 " --> pdb=" O ASP F 692 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER F 703 " --> pdb=" O THR F 699 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL F 704 " --> pdb=" O ASP F 700 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL F 705 " --> pdb=" O HIS F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 767 removed outlier: 3.671A pdb=" N VAL F 763 " --> pdb=" O THR F 760 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP F 764 " --> pdb=" O SER F 761 " (cutoff:3.500A) Proline residue: F 765 - end of helix No H-bonds generated for 'chain 'F' and resid 760 through 767' Processing helix chain 'F' and resid 796 through 807 removed outlier: 3.511A pdb=" N SER F 801 " --> pdb=" O SER F 797 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER F 803 " --> pdb=" O THR F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 823 removed outlier: 4.274A pdb=" N ILE F 820 " --> pdb=" O PRO F 816 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN F 821 " --> pdb=" O ASP F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 825 through 827 No H-bonds generated for 'chain 'F' and resid 825 through 827' Processing helix chain 'F' and resid 852 through 858 Processing helix chain 'F' and resid 860 through 863 No H-bonds generated for 'chain 'F' and resid 860 through 863' Processing helix chain 'F' and resid 880 through 889 Processing helix chain 'F' and resid 904 through 911 Processing helix chain 'F' and resid 948 through 950 No H-bonds generated for 'chain 'F' and resid 948 through 950' Processing helix chain 'F' and resid 962 through 970 removed outlier: 3.806A pdb=" N GLN F 966 " --> pdb=" O ASP F 962 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 989 removed outlier: 3.580A pdb=" N ILE F 986 " --> pdb=" O ALA F 982 " (cutoff:3.500A) Processing helix chain 'F' and resid 996 through 1002 removed outlier: 3.757A pdb=" N LEU F1000 " --> pdb=" O ASP F 996 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1040 No H-bonds generated for 'chain 'F' and resid 1038 through 1040' Processing helix chain 'F' and resid 1049 through 1062 removed outlier: 4.108A pdb=" N ARG F1053 " --> pdb=" O GLU F1049 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F1057 " --> pdb=" O ARG F1053 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F1060 " --> pdb=" O SER F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1149 through 1162 removed outlier: 3.628A pdb=" N ILE F1156 " --> pdb=" O ALA F1152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F1160 " --> pdb=" O ILE F1156 " (cutoff:3.500A) Processing helix chain 'F' and resid 1209 through 1211 No H-bonds generated for 'chain 'F' and resid 1209 through 1211' Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.699A pdb=" N ASP G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 120 " --> pdb=" O SER G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 194 No H-bonds generated for 'chain 'G' and resid 191 through 194' Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 244 through 259 removed outlier: 3.528A pdb=" N VAL G 248 " --> pdb=" O ALA G 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 251 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 252 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 254 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 258 " --> pdb=" O LEU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 298 through 301 Processing helix chain 'G' and resid 308 through 318 Processing helix chain 'G' and resid 352 through 363 removed outlier: 3.779A pdb=" N VAL G 357 " --> pdb=" O PHE G 353 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 362 " --> pdb=" O LEU G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.697A pdb=" N GLN G 380 " --> pdb=" O LYS G 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA G 381 " --> pdb=" O ALA G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 397 No H-bonds generated for 'chain 'G' and resid 395 through 397' Processing helix chain 'G' and resid 405 through 418 removed outlier: 3.598A pdb=" N ILE G 409 " --> pdb=" O HIS G 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 410 " --> pdb=" O ASP G 406 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET G 413 " --> pdb=" O ILE G 409 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 416 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 417 " --> pdb=" O MET G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.919A pdb=" N GLU G 423 " --> pdb=" O PRO G 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 426 " --> pdb=" O GLU G 423 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL G 427 " --> pdb=" O GLY G 424 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 431 " --> pdb=" O GLN G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 466 removed outlier: 4.286A pdb=" N ARG G 461 " --> pdb=" O SER G 458 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 463 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER G 464 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL G 466 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 486 removed outlier: 3.755A pdb=" N LEU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 485 " --> pdb=" O ALA G 481 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL G 486 " --> pdb=" O ILE G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 520 removed outlier: 3.745A pdb=" N ILE G 508 " --> pdb=" O PRO G 505 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL G 509 " --> pdb=" O SER G 506 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 510 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 515 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 516 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE G 517 " --> pdb=" O PHE G 514 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE G 520 " --> pdb=" O PHE G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 526 Processing helix chain 'G' and resid 529 through 543 removed outlier: 3.676A pdb=" N VAL G 535 " --> pdb=" O ASP G 531 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU G 538 " --> pdb=" O ASN G 534 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 542 " --> pdb=" O LEU G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 554 removed outlier: 3.963A pdb=" N GLY G 549 " --> pdb=" O PRO G 545 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE G 550 " --> pdb=" O VAL G 546 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE G 551 " --> pdb=" O GLU G 547 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 554 " --> pdb=" O ILE G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 590 No H-bonds generated for 'chain 'G' and resid 588 through 590' Processing helix chain 'G' and resid 598 through 604 Processing helix chain 'G' and resid 617 through 620 No H-bonds generated for 'chain 'G' and resid 617 through 620' Processing helix chain 'G' and resid 649 through 670 removed outlier: 3.520A pdb=" N THR G 654 " --> pdb=" O SER G 650 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR G 658 " --> pdb=" O THR G 654 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN G 661 " --> pdb=" O ALA G 657 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN G 664 " --> pdb=" O ALA G 660 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP G 670 " --> pdb=" O ARG G 666 " (cutoff:3.500A) Processing helix chain 'G' and resid 674 through 684 removed outlier: 3.871A pdb=" N THR G 680 " --> pdb=" O THR G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 686 through 701 removed outlier: 3.541A pdb=" N ASN G 693 " --> pdb=" O THR G 689 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 694 " --> pdb=" O GLN G 690 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL G 696 " --> pdb=" O ASP G 692 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA G 697 " --> pdb=" O ASN G 693 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP G 700 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS G 701 " --> pdb=" O ALA G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 709 Processing helix chain 'G' and resid 760 through 767 removed outlier: 3.839A pdb=" N VAL G 763 " --> pdb=" O THR G 760 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP G 764 " --> pdb=" O SER G 761 " (cutoff:3.500A) Proline residue: G 765 - end of helix No H-bonds generated for 'chain 'G' and resid 760 through 767' Processing helix chain 'G' and resid 796 through 812 removed outlier: 3.641A pdb=" N VAL G 806 " --> pdb=" O GLN G 802 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER G 811 " --> pdb=" O ALA G 807 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 812 " --> pdb=" O GLN G 808 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 removed outlier: 3.510A pdb=" N PHE G 819 " --> pdb=" O LEU G 815 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE G 820 " --> pdb=" O PRO G 816 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN G 821 " --> pdb=" O ASP G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 852 through 858 removed outlier: 3.615A pdb=" N HIS G 858 " --> pdb=" O GLN G 854 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 866 removed outlier: 3.503A pdb=" N HIS G 864 " --> pdb=" O ARG G 860 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 865 " --> pdb=" O GLU G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 880 through 889 removed outlier: 3.683A pdb=" N ALA G 885 " --> pdb=" O ASP G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 904 through 913 removed outlier: 3.532A pdb=" N THR G 908 " --> pdb=" O GLY G 904 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 909 " --> pdb=" O SER G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 948 through 950 No H-bonds generated for 'chain 'G' and resid 948 through 950' Processing helix chain 'G' and resid 962 through 970 removed outlier: 3.722A pdb=" N GLN G 966 " --> pdb=" O ASP G 962 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 967 " --> pdb=" O ALA G 963 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA G 969 " --> pdb=" O ARG G 965 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 989 removed outlier: 3.513A pdb=" N ILE G 986 " --> pdb=" O ALA G 982 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN G 988 " --> pdb=" O GLU G 984 " (cutoff:3.500A) Processing helix chain 'G' and resid 998 through 1002 Processing helix chain 'G' and resid 1038 through 1040 No H-bonds generated for 'chain 'G' and resid 1038 through 1040' Processing helix chain 'G' and resid 1050 through 1062 removed outlier: 3.801A pdb=" N LEU G1055 " --> pdb=" O ARG G1051 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G1057 " --> pdb=" O ARG G1053 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G1060 " --> pdb=" O SER G1056 " (cutoff:3.500A) Processing helix chain 'G' and resid 1149 through 1162 removed outlier: 3.577A pdb=" N ILE G1160 " --> pdb=" O ILE G1156 " (cutoff:3.500A) Processing helix chain 'G' and resid 1262 through 1265 Processing sheet with id= A, first strand: chain 'A' and resid 54 through 57 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 185 Processing sheet with id= C, first strand: chain 'A' and resid 475 through 479 removed outlier: 4.331A pdb=" N LYS A 475 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 543 through 546 Processing sheet with id= E, first strand: chain 'A' and resid 621 through 623 Processing sheet with id= F, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.876A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 792 through 795 removed outlier: 3.631A pdb=" N SER A 829 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1022 through 1025 Processing sheet with id= I, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.841A pdb=" N ALA A 267 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.240A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 206 through 208 Processing sheet with id= L, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.609A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.710A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1300 through 1305 removed outlier: 3.753A pdb=" N ILE C 343 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 331 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 347 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 329 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 388 through 390 Processing sheet with id= P, first strand: chain 'C' and resid 440 through 442 Processing sheet with id= Q, first strand: chain 'C' and resid 558 through 560 Processing sheet with id= R, first strand: chain 'C' and resid 612 through 615 Processing sheet with id= S, first strand: chain 'C' and resid 732 through 735 Processing sheet with id= T, first strand: chain 'C' and resid 829 through 832 Processing sheet with id= U, first strand: chain 'C' and resid 833 through 835 removed outlier: 6.127A pdb=" N VAL C 917 " --> pdb=" O THR C 850 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 1230 through 1232 removed outlier: 3.501A pdb=" N VAL C1165 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C1097 " --> pdb=" O HIS C1138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR C1140 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL C1099 " --> pdb=" O THR C1140 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1107 through 1110 Processing sheet with id= X, first strand: chain 'C' and resid 1172 through 1178 removed outlier: 3.503A pdb=" N GLU C1176 " --> pdb=" O LEU C1204 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 164 through 170 removed outlier: 3.623A pdb=" N VAL C 203 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C1242 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 206 " --> pdb=" O ARG C1240 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG C1240 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.801A pdb=" N THR D 145 " --> pdb=" O VAL D1317 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 1301 through 1305 removed outlier: 3.751A pdb=" N ILE D 343 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 331 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 347 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU D 329 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 388 through 390 Processing sheet with id= AC, first strand: chain 'D' and resid 440 through 442 Processing sheet with id= AD, first strand: chain 'D' and resid 558 through 560 Processing sheet with id= AE, first strand: chain 'D' and resid 612 through 615 removed outlier: 3.519A pdb=" N ILE D 635 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 732 through 735 Processing sheet with id= AG, first strand: chain 'D' and resid 944 through 947 removed outlier: 7.805A pdb=" N VAL D 831 " --> pdb=" O THR D 851 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR D 851 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1230 through 1232 removed outlier: 6.013A pdb=" N VAL D1097 " --> pdb=" O HIS D1138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR D1140 " --> pdb=" O VAL D1097 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D1099 " --> pdb=" O THR D1140 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 1106 through 1110 Processing sheet with id= AJ, first strand: chain 'D' and resid 1172 through 1179 Processing sheet with id= AK, first strand: chain 'D' and resid 164 through 170 removed outlier: 3.679A pdb=" N VAL D 203 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET D1242 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D 206 " --> pdb=" O ARG D1240 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG D1240 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 1300 through 1305 removed outlier: 3.605A pdb=" N GLU E 331 " --> pdb=" O GLY E 345 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 347 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 329 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 388 through 390 Processing sheet with id= AN, first strand: chain 'E' and resid 558 through 560 removed outlier: 3.563A pdb=" N GLU E 567 " --> pdb=" O THR E 559 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 612 through 615 Processing sheet with id= AP, first strand: chain 'E' and resid 732 through 735 removed outlier: 3.661A pdb=" N ARG E1020 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 944 through 947 removed outlier: 7.910A pdb=" N VAL E 831 " --> pdb=" O THR E 851 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR E 851 " --> pdb=" O VAL E 831 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL E 917 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 1230 through 1232 removed outlier: 6.256A pdb=" N VAL E1097 " --> pdb=" O HIS E1138 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR E1140 " --> pdb=" O VAL E1097 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E1099 " --> pdb=" O THR E1140 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 1107 through 1110 Processing sheet with id= AT, first strand: chain 'E' and resid 1172 through 1179 Processing sheet with id= AU, first strand: chain 'E' and resid 164 through 170 removed outlier: 3.594A pdb=" N VAL E 203 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET E1242 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 206 " --> pdb=" O ARG E1240 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG E1240 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.588A pdb=" N THR F 145 " --> pdb=" O VAL F1317 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'F' and resid 1300 through 1305 removed outlier: 3.581A pdb=" N ILE F 343 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 331 " --> pdb=" O GLY F 345 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 347 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU F 329 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 388 through 390 Processing sheet with id= AY, first strand: chain 'F' and resid 558 through 560 Processing sheet with id= AZ, first strand: chain 'F' and resid 612 through 615 Processing sheet with id= BA, first strand: chain 'F' and resid 732 through 735 Processing sheet with id= BB, first strand: chain 'F' and resid 944 through 947 removed outlier: 7.755A pdb=" N VAL F 831 " --> pdb=" O THR F 851 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR F 851 " --> pdb=" O VAL F 831 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 917 " --> pdb=" O THR F 850 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 1230 through 1232 removed outlier: 6.288A pdb=" N VAL F1097 " --> pdb=" O HIS F1138 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR F1140 " --> pdb=" O VAL F1097 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F1099 " --> pdb=" O THR F1140 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 1106 through 1110 Processing sheet with id= BE, first strand: chain 'F' and resid 1176 through 1179 Processing sheet with id= BF, first strand: chain 'F' and resid 164 through 170 removed outlier: 3.873A pdb=" N MET F1242 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 206 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG F1240 " --> pdb=" O ILE F 206 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'G' and resid 145 through 147 removed outlier: 3.836A pdb=" N THR G 145 " --> pdb=" O VAL G1317 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 1300 through 1305 removed outlier: 3.811A pdb=" N ILE G 343 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU G 331 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA G 347 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU G 329 " --> pdb=" O ALA G 347 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 388 through 390 Processing sheet with id= BJ, first strand: chain 'G' and resid 584 through 586 Processing sheet with id= BK, first strand: chain 'G' and resid 612 through 615 Processing sheet with id= BL, first strand: chain 'G' and resid 732 through 735 Processing sheet with id= BM, first strand: chain 'G' and resid 944 through 947 removed outlier: 7.720A pdb=" N VAL G 831 " --> pdb=" O THR G 851 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR G 851 " --> pdb=" O VAL G 831 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL G 917 " --> pdb=" O THR G 850 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'G' and resid 1230 through 1232 removed outlier: 6.209A pdb=" N VAL G1097 " --> pdb=" O HIS G1138 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR G1140 " --> pdb=" O VAL G1097 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL G1099 " --> pdb=" O THR G1140 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'G' and resid 1107 through 1110 Processing sheet with id= BP, first strand: chain 'G' and resid 1172 through 1179 removed outlier: 3.501A pdb=" N GLU G1176 " --> pdb=" O LEU G1204 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'G' and resid 164 through 170 1401 hydrogen bonds defined for protein. 3567 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: 20.41 Time building geometry restraints manager: 19.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 3 1.14 - 1.31: 10274 1.31 - 1.48: 25564 1.48 - 1.65: 26349 1.65 - 1.82: 461 Bond restraints: 62651 Sorted by residual: bond pdb=" C TYR A1083 " pdb=" N HIS A1084 " ideal model delta sigma weight residual 1.332 1.588 -0.256 8.30e-03 1.45e+04 9.52e+02 bond pdb=" C3' MG7 A1302 " pdb=" O3' MG7 A1302 " ideal model delta sigma weight residual 1.417 0.964 0.453 1.50e-02 4.44e+03 9.12e+02 bond pdb=" C5' U t 1 " pdb=" C4' U t 1 " ideal model delta sigma weight residual 1.508 1.131 0.377 1.50e-02 4.44e+03 6.33e+02 bond pdb=" C2' MG7 A1302 " pdb=" O2' MG7 A1302 " ideal model delta sigma weight residual 1.420 1.097 0.323 1.50e-02 4.44e+03 4.62e+02 bond pdb=" C2' MG7 A1302 " pdb=" C3' MG7 A1302 " ideal model delta sigma weight residual 1.523 1.214 0.309 1.50e-02 4.44e+03 4.24e+02 ... (remaining 62646 not shown) Histogram of bond angle deviations from ideal: 68.31 - 87.26: 5 87.26 - 106.22: 1850 106.22 - 125.17: 82327 125.17 - 144.13: 1051 144.13 - 163.09: 4 Bond angle restraints: 85237 Sorted by residual: angle pdb=" O3' U t 1 " pdb=" C3' U t 1 " pdb=" C2' U t 1 " ideal model delta sigma weight residual 113.70 68.31 45.39 1.50e+00 4.44e-01 9.16e+02 angle pdb=" C5' U t 1 " pdb=" C4' U t 1 " pdb=" C3' U t 1 " ideal model delta sigma weight residual 116.00 157.03 -41.03 1.50e+00 4.44e-01 7.48e+02 angle pdb=" C4' U t 1 " pdb=" C3' U t 1 " pdb=" O3' U t 1 " ideal model delta sigma weight residual 113.00 145.42 -32.42 1.50e+00 4.44e-01 4.67e+02 angle pdb=" O2' U t 2 " pdb=" C2' U t 2 " pdb=" C1' U t 2 " ideal model delta sigma weight residual 108.40 76.66 31.74 1.50e+00 4.44e-01 4.48e+02 angle pdb=" C5' U t 1 " pdb=" C4' U t 1 " pdb=" O4' U t 1 " ideal model delta sigma weight residual 109.80 81.39 28.41 1.50e+00 4.44e-01 3.59e+02 ... (remaining 85232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 37242 30.97 - 61.94: 542 61.94 - 92.91: 86 92.91 - 123.88: 3 123.88 - 154.85: 4 Dihedral angle restraints: 37877 sinusoidal: 15156 harmonic: 22721 Sorted by residual: dihedral pdb=" CA ILE C 475 " pdb=" C ILE C 475 " pdb=" N SER C 476 " pdb=" CA SER C 476 " ideal model delta harmonic sigma weight residual -180.00 -45.47 -134.53 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA PRO A 821 " pdb=" C PRO A 821 " pdb=" N ASP A 822 " pdb=" CA ASP A 822 " ideal model delta harmonic sigma weight residual -180.00 -50.23 -129.77 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA ASN B 64 " pdb=" C ASN B 64 " pdb=" N GLY B 65 " pdb=" CA GLY B 65 " ideal model delta harmonic sigma weight residual -180.00 -58.10 -121.90 0 5.00e+00 4.00e-02 5.94e+02 ... (remaining 37874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 9734 0.396 - 0.792: 11 0.792 - 1.188: 3 1.188 - 1.584: 1 1.584 - 1.980: 3 Chirality restraints: 9752 Sorted by residual: chirality pdb=" C2' MG7 A1302 " pdb=" C1' MG7 A1302 " pdb=" C3' MG7 A1302 " pdb=" O2' MG7 A1302 " both_signs ideal model delta sigma weight residual False -2.75 -0.77 -1.98 2.00e-01 2.50e+01 9.80e+01 chirality pdb=" C4' U t 1 " pdb=" C5' U t 1 " pdb=" O4' U t 1 " pdb=" C3' U t 1 " both_signs ideal model delta sigma weight residual False -2.50 -0.85 -1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" C3' MG7 A1302 " pdb=" C2' MG7 A1302 " pdb=" C4' MG7 A1302 " pdb=" O3' MG7 A1302 " both_signs ideal model delta sigma weight residual False -2.48 -0.88 -1.60 2.00e-01 2.50e+01 6.40e+01 ... (remaining 9749 not shown) Planarity restraints: 11061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' A2M A1304 " -0.005 2.00e-02 2.50e+03 2.76e-01 1.72e+03 pdb=" C4' A2M A1304 " -0.219 2.00e-02 2.50e+03 pdb=" O4' A2M A1304 " -0.338 2.00e-02 2.50e+03 pdb=" C3' A2M A1304 " 0.394 2.00e-02 2.50e+03 pdb=" O3' A2M A1304 " 0.134 2.00e-02 2.50e+03 pdb=" C2' A2M A1304 " 0.193 2.00e-02 2.50e+03 pdb=" O2' A2M A1304 " -0.358 2.00e-02 2.50e+03 pdb=" C1' A2M A1304 " -0.189 2.00e-02 2.50e+03 pdb=" N9 A2M A1304 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UTP A1306 " 0.291 2.00e-02 2.50e+03 2.75e-01 1.70e+03 pdb=" C2' UTP A1306 " -0.144 2.00e-02 2.50e+03 pdb=" C3' UTP A1306 " -0.444 2.00e-02 2.50e+03 pdb=" C4' UTP A1306 " 0.351 2.00e-02 2.50e+03 pdb=" C5' UTP A1306 " -0.157 2.00e-02 2.50e+03 pdb=" N1 UTP A1306 " -0.352 2.00e-02 2.50e+03 pdb=" O2' UTP A1306 " 0.240 2.00e-02 2.50e+03 pdb=" O3' UTP A1306 " -0.004 2.00e-02 2.50e+03 pdb=" O4' UTP A1306 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A2M A1304 " -0.570 2.00e-02 2.50e+03 2.24e-01 1.38e+03 pdb=" N9 A2M A1304 " 0.173 2.00e-02 2.50e+03 pdb=" C8 A2M A1304 " 0.267 2.00e-02 2.50e+03 pdb=" N7 A2M A1304 " 0.126 2.00e-02 2.50e+03 pdb=" C5 A2M A1304 " 0.067 2.00e-02 2.50e+03 pdb=" C6 A2M A1304 " -0.082 2.00e-02 2.50e+03 pdb=" N6 A2M A1304 " -0.195 2.00e-02 2.50e+03 pdb=" N1 A2M A1304 " -0.103 2.00e-02 2.50e+03 pdb=" C2 A2M A1304 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A2M A1304 " 0.140 2.00e-02 2.50e+03 pdb=" C4 A2M A1304 " 0.174 2.00e-02 2.50e+03 ... (remaining 11058 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 10 2.06 - 2.77: 12190 2.77 - 3.48: 80496 3.48 - 4.19: 145167 4.19 - 4.90: 248277 Nonbonded interactions: 486140 Sorted by model distance: nonbonded pdb=" OH TYR A1083 " pdb=" O3' U t 5 " model vdw 1.345 2.440 nonbonded pdb=" NE2 HIS A1084 " pdb=" O3B 3PO p 1 " model vdw 1.596 2.520 nonbonded pdb=" OH TYR A1083 " pdb=" C3' U t 5 " model vdw 1.701 3.470 nonbonded pdb=" O2 U t 1 " pdb=" OP2 U t 2 " model vdw 1.767 3.040 nonbonded pdb=" O ASN A1082 " pdb=" CD1 TYR A1083 " model vdw 1.900 3.340 ... (remaining 486135 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 'C' and (resid 135 through 778 or resid 787 through 1333)) selection = (chain 'D' and resid 135 through 1333) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 135 through 1333) } 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: 0.770 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: 0.070 Extract box with map and model: 5.300 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 123.120 Find NCS groups from input model: 4.610 Set up NCS constraints: 0.190 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 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 : 0.009 0.453 62651 Z= 0.603 Angle : 1.218 46.711 85237 Z= 0.676 Chirality : 0.073 1.980 9752 Planarity : 0.010 0.484 11061 Dihedral : 11.623 154.848 23177 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.33 % Favored : 93.34 % Rotamer: Outliers : 1.25 % Allowed : 4.28 % Favored : 94.47 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.38 % Twisted Proline : 0.85 % Twisted General : 0.95 % 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: -4.88 (0.07), residues: 7697 helix: -4.32 (0.04), residues: 2730 sheet: -2.70 (0.14), residues: 984 loop : -2.51 (0.08), residues: 3983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP G 543 HIS 0.029 0.002 HIS A 648 PHE 0.058 0.003 PHE B 159 TYR 0.033 0.003 TYR A 870 ARG 0.024 0.001 ARG A 946 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2691 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 2607 time to evaluate : 5.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.7551 (t-90) cc_final: 0.7138 (t-90) REVERT: A 92 GLU cc_start: 0.7568 (mp0) cc_final: 0.7304 (tm-30) REVERT: A 102 ASP cc_start: 0.7653 (p0) cc_final: 0.7118 (p0) REVERT: A 125 LEU cc_start: 0.7835 (tp) cc_final: 0.7618 (tp) REVERT: A 137 GLN cc_start: 0.7263 (mm-40) cc_final: 0.7056 (mm-40) REVERT: A 215 THR cc_start: 0.6846 (m) cc_final: 0.6469 (m) REVERT: A 252 ILE cc_start: 0.7772 (mm) cc_final: 0.7470 (mm) REVERT: A 259 GLU cc_start: 0.7410 (tt0) cc_final: 0.6624 (tt0) REVERT: A 286 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 362 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5472 (mp0) REVERT: A 456 PHE cc_start: 0.7670 (m-10) cc_final: 0.7320 (m-80) REVERT: A 485 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7400 (pmt170) REVERT: A 502 MET cc_start: 0.8608 (tpt) cc_final: 0.8298 (tpp) REVERT: A 542 LEU cc_start: 0.6511 (pp) cc_final: 0.6178 (pp) REVERT: A 568 LEU cc_start: 0.7524 (mt) cc_final: 0.7172 (mt) REVERT: A 587 MET cc_start: 0.7407 (mtt) cc_final: 0.6924 (mtp) REVERT: A 629 GLN cc_start: 0.7781 (tt0) cc_final: 0.7463 (tt0) REVERT: A 775 GLU cc_start: 0.6925 (mp0) cc_final: 0.6627 (mp0) REVERT: A 860 ASP cc_start: 0.7287 (p0) cc_final: 0.6817 (t0) REVERT: A 889 SER cc_start: 0.8874 (m) cc_final: 0.8328 (p) REVERT: A 919 GLU cc_start: 0.7733 (tp30) cc_final: 0.7408 (tp30) REVERT: A 922 LYS cc_start: 0.7674 (tptp) cc_final: 0.6981 (mptt) REVERT: A 963 LEU cc_start: 0.7925 (tp) cc_final: 0.7224 (tt) REVERT: B 47 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7369 (ttmt) REVERT: B 139 THR cc_start: 0.8622 (m) cc_final: 0.8410 (m) REVERT: B 146 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 170 ASN cc_start: 0.8368 (m110) cc_final: 0.8090 (m110) REVERT: B 199 ARG cc_start: 0.8413 (ttm170) cc_final: 0.7964 (tmm-80) REVERT: B 204 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7494 (ttp-110) REVERT: B 269 MET cc_start: 0.7672 (ptm) cc_final: 0.7384 (ptp) REVERT: B 285 ASP cc_start: 0.7056 (p0) cc_final: 0.6848 (p0) REVERT: B 343 ASN cc_start: 0.7601 (t160) cc_final: 0.7162 (t0) REVERT: B 452 MET cc_start: 0.7713 (tpt) cc_final: 0.7320 (tpp) REVERT: B 461 GLU cc_start: 0.8235 (tt0) cc_final: 0.7781 (tt0) REVERT: B 490 HIS cc_start: 0.8155 (m90) cc_final: 0.7790 (m-70) REVERT: B 542 HIS cc_start: 0.8539 (m90) cc_final: 0.8253 (m-70) REVERT: C 329 LEU cc_start: 0.7743 (tp) cc_final: 0.7516 (tp) REVERT: C 371 THR cc_start: 0.6578 (p) cc_final: 0.6218 (p) REVERT: C 377 LYS cc_start: 0.8892 (mttt) cc_final: 0.8120 (mtpt) REVERT: C 419 TYR cc_start: 0.8052 (m-80) cc_final: 0.7713 (m-80) REVERT: C 532 ILE cc_start: 0.8503 (mt) cc_final: 0.8161 (mt) REVERT: C 641 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7518 (ppt170) REVERT: C 715 ASN cc_start: 0.6159 (m-40) cc_final: 0.5926 (m-40) REVERT: C 828 ASP cc_start: 0.4865 (m-30) cc_final: 0.4226 (m-30) REVERT: C 1227 MET cc_start: 0.7652 (mmt) cc_final: 0.7415 (mtm) REVERT: C 1231 TYR cc_start: 0.7903 (m-80) cc_final: 0.7482 (m-80) REVERT: C 1249 ASN cc_start: 0.8292 (p0) cc_final: 0.7863 (p0) REVERT: C 1265 MET cc_start: 0.7404 (mtm) cc_final: 0.6961 (mtm) REVERT: C 1328 ILE cc_start: 0.8654 (mt) cc_final: 0.8440 (mt) REVERT: D 214 ASP cc_start: 0.7770 (p0) cc_final: 0.7437 (p0) REVERT: D 491 ASN cc_start: 0.7849 (m110) cc_final: 0.7647 (m110) REVERT: D 629 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.6405 (ttp-110) REVERT: D 742 LYS cc_start: 0.8398 (tptm) cc_final: 0.8187 (tptp) REVERT: D 835 TYR cc_start: 0.7766 (m-10) cc_final: 0.7370 (m-10) REVERT: D 836 GLN cc_start: 0.8674 (mp10) cc_final: 0.7965 (mp10) REVERT: D 873 TYR cc_start: 0.7557 (m-80) cc_final: 0.7185 (m-80) REVERT: D 926 VAL cc_start: 0.8431 (t) cc_final: 0.8189 (m) REVERT: D 1038 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7849 (tt0) REVERT: D 1072 ASP cc_start: 0.7270 (p0) cc_final: 0.4485 (t0) REVERT: D 1078 TYR cc_start: 0.7839 (t80) cc_final: 0.7590 (t80) REVERT: D 1096 TYR cc_start: 0.6505 (m-10) cc_final: 0.5767 (m-80) REVERT: D 1161 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8280 (mmtp) REVERT: D 1265 MET cc_start: 0.7498 (mtm) cc_final: 0.7164 (mtm) REVERT: D 1279 SER cc_start: 0.8291 (m) cc_final: 0.7992 (m) REVERT: D 1296 ILE cc_start: 0.8776 (mm) cc_final: 0.8462 (mm) REVERT: E 243 GLN cc_start: 0.8002 (mt0) cc_final: 0.7385 (tp40) REVERT: E 262 ASN cc_start: 0.7803 (p0) cc_final: 0.7501 (p0) REVERT: E 438 ASN cc_start: 0.7569 (t0) cc_final: 0.7343 (m-40) REVERT: E 557 THR cc_start: 0.7988 (p) cc_final: 0.7760 (p) REVERT: E 578 SER cc_start: 0.8258 (m) cc_final: 0.7991 (t) REVERT: E 745 ILE cc_start: 0.7160 (mt) cc_final: 0.6588 (tt) REVERT: E 766 ILE cc_start: 0.6378 (mt) cc_final: 0.6056 (mt) REVERT: E 837 THR cc_start: 0.8070 (p) cc_final: 0.7858 (t) REVERT: E 924 ASP cc_start: 0.8369 (t0) cc_final: 0.7936 (t0) REVERT: E 1149 LYS cc_start: 0.7597 (tttp) cc_final: 0.6551 (ttpt) REVERT: E 1265 MET cc_start: 0.8191 (mtm) cc_final: 0.7895 (mtm) REVERT: F 142 ASP cc_start: 0.7330 (t70) cc_final: 0.7008 (p0) REVERT: F 209 ASN cc_start: 0.8782 (t0) cc_final: 0.8437 (t0) REVERT: F 438 ASN cc_start: 0.8172 (t0) cc_final: 0.7879 (t0) REVERT: F 508 ILE cc_start: 0.7312 (tp) cc_final: 0.6903 (tt) REVERT: F 561 ASN cc_start: 0.8612 (t0) cc_final: 0.8209 (t0) REVERT: F 701 HIS cc_start: 0.7942 (t70) cc_final: 0.7670 (t70) REVERT: F 712 PHE cc_start: 0.8162 (m-10) cc_final: 0.7909 (m-80) REVERT: F 808 GLN cc_start: 0.7478 (tt0) cc_final: 0.7118 (tt0) REVERT: F 1189 ASP cc_start: 0.7375 (m-30) cc_final: 0.7165 (m-30) REVERT: F 1231 TYR cc_start: 0.8012 (m-80) cc_final: 0.7788 (m-80) REVERT: F 1278 TYR cc_start: 0.6631 (m-80) cc_final: 0.6287 (m-80) REVERT: G 242 GLU cc_start: 0.7278 (pm20) cc_final: 0.6915 (pm20) REVERT: G 324 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8198 (ptmm) REVERT: G 398 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7860 (mpt180) REVERT: G 572 ASN cc_start: 0.7552 (t0) cc_final: 0.7337 (t0) REVERT: G 581 LEU cc_start: 0.8811 (mt) cc_final: 0.8592 (mt) REVERT: G 800 LEU cc_start: 0.7286 (tp) cc_final: 0.7011 (tp) REVERT: G 802 GLN cc_start: 0.7879 (mt0) cc_final: 0.7578 (mt0) REVERT: G 836 GLN cc_start: 0.8473 (mp10) cc_final: 0.8258 (mp10) REVERT: G 909 TYR cc_start: 0.7751 (t80) cc_final: 0.7499 (t80) REVERT: G 986 ILE cc_start: 0.6056 (mt) cc_final: 0.5385 (tt) REVERT: G 1014 MET cc_start: 0.7355 (mmm) cc_final: 0.7028 (mmm) REVERT: G 1085 ASP cc_start: 0.7116 (p0) cc_final: 0.6002 (t0) REVERT: G 1144 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7700 (ttp-110) REVERT: G 1231 TYR cc_start: 0.7701 (m-80) cc_final: 0.7128 (m-80) REVERT: G 1318 GLU cc_start: 0.6046 (tt0) cc_final: 0.5723 (tt0) outliers start: 84 outliers final: 28 residues processed: 2652 average time/residue: 0.5871 time to fit residues: 2588.6163 Evaluate side-chains 1725 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1694 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1022 HIS Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 995 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain E residue 1076 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 0.6980 chunk 582 optimal weight: 7.9990 chunk 323 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 393 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 602 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 366 optimal weight: 6.9990 chunk 448 optimal weight: 3.9990 chunk 698 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 126 HIS A 274 GLN A 312 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 586 ASN A 617 GLN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A1020 HIS B 170 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 343 ASN B 346 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 156 GLN C 292 ASN C 346 HIS C 456 ASN C 533 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 GLN C 942 HIS ** C 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 GLN D 346 HIS D 430 ASN D 661 ASN D 715 ASN D 821 ASN D 954 GLN D1015 GLN D1112 ASN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN E 292 ASN E 346 HIS ** E 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 HIS E 698 HIS E 724 HIS ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 854 GLN E 867 ASN E 937 ASN E 988 GLN E1112 ASN F 346 HIS ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 HIS ** F 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 913 ASN ** F 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1112 ASN ** F1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1234 GLN F1332 ASN G 124 GLN G 319 GLN G 346 HIS G 430 ASN G 452 ASN G 640 GLN G 731 GLN G 942 HIS ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1112 ASN G1121 HIS G1248 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 62651 Z= 0.180 Angle : 0.698 19.747 85237 Z= 0.352 Chirality : 0.045 0.255 9752 Planarity : 0.005 0.076 11061 Dihedral : 8.212 167.567 8750 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.64 % Favored : 95.13 % Rotamer: Outliers : 3.62 % Allowed : 14.29 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.37 % 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: -3.71 (0.08), residues: 7697 helix: -3.01 (0.07), residues: 2720 sheet: -2.30 (0.15), residues: 979 loop : -2.03 (0.09), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 445 HIS 0.011 0.001 HIS F 407 PHE 0.025 0.002 PHE C 353 TYR 0.043 0.002 TYR A1083 ARG 0.008 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2098 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1854 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.7420 (t-90) cc_final: 0.6785 (t-90) REVERT: A 102 ASP cc_start: 0.7691 (p0) cc_final: 0.7415 (p0) REVERT: A 133 MET cc_start: 0.7463 (ttp) cc_final: 0.6889 (tpp) REVERT: A 137 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6945 (mm-40) REVERT: A 215 THR cc_start: 0.7236 (m) cc_final: 0.6831 (m) REVERT: A 379 GLU cc_start: 0.7441 (pt0) cc_final: 0.7198 (pt0) REVERT: A 421 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7176 (tt) REVERT: A 475 LYS cc_start: 0.5981 (ptpp) cc_final: 0.5526 (pttt) REVERT: A 484 ARG cc_start: 0.7648 (ttt180) cc_final: 0.7264 (ttt-90) REVERT: A 485 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7794 (ptt-90) REVERT: A 502 MET cc_start: 0.8573 (tpt) cc_final: 0.8313 (tpp) REVERT: A 659 ASN cc_start: 0.7745 (t0) cc_final: 0.7379 (t0) REVERT: A 817 TYR cc_start: 0.7860 (m-10) cc_final: 0.7645 (m-80) REVERT: A 854 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6099 (p0) REVERT: A 857 PHE cc_start: 0.8356 (m-10) cc_final: 0.7979 (m-10) REVERT: A 860 ASP cc_start: 0.7589 (p0) cc_final: 0.7102 (t0) REVERT: A 883 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: A 889 SER cc_start: 0.8725 (m) cc_final: 0.8492 (p) REVERT: A 899 GLU cc_start: 0.8068 (tt0) cc_final: 0.7490 (mt-10) REVERT: A 919 GLU cc_start: 0.7710 (tp30) cc_final: 0.7409 (tp30) REVERT: A 922 LYS cc_start: 0.7897 (tptp) cc_final: 0.7376 (mptt) REVERT: B 154 LEU cc_start: 0.7267 (mt) cc_final: 0.6846 (mp) REVERT: B 198 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7659 (tt) REVERT: B 204 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7592 (ttp-110) REVERT: B 280 LEU cc_start: 0.7914 (pp) cc_final: 0.7704 (pp) REVERT: B 461 GLU cc_start: 0.8245 (tt0) cc_final: 0.7833 (tt0) REVERT: B 490 HIS cc_start: 0.8409 (m90) cc_final: 0.7889 (m-70) REVERT: B 510 ILE cc_start: 0.7637 (pp) cc_final: 0.7363 (pp) REVERT: C 123 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7275 (mm-30) REVERT: C 135 LYS cc_start: 0.4019 (pptt) cc_final: 0.3238 (mttt) REVERT: C 184 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 262 ASN cc_start: 0.7112 (p0) cc_final: 0.6894 (p0) REVERT: C 329 LEU cc_start: 0.7665 (tp) cc_final: 0.7348 (tp) REVERT: C 361 ASN cc_start: 0.8260 (m-40) cc_final: 0.7951 (m-40) REVERT: C 375 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7620 (mtt90) REVERT: C 377 LYS cc_start: 0.8881 (mttt) cc_final: 0.8183 (mtpt) REVERT: C 419 TYR cc_start: 0.8139 (m-80) cc_final: 0.7660 (m-80) REVERT: C 760 THR cc_start: 0.8856 (p) cc_final: 0.8579 (t) REVERT: C 828 ASP cc_start: 0.4551 (m-30) cc_final: 0.3564 (m-30) REVERT: C 844 ASP cc_start: 0.8541 (t0) cc_final: 0.7990 (p0) REVERT: C 845 GLU cc_start: 0.6762 (tt0) cc_final: 0.6397 (tt0) REVERT: C 867 ASN cc_start: 0.8827 (t0) cc_final: 0.8599 (t0) REVERT: C 1085 ASP cc_start: 0.7501 (p0) cc_final: 0.7013 (p0) REVERT: C 1091 ASP cc_start: 0.7688 (m-30) cc_final: 0.7468 (m-30) REVERT: C 1231 TYR cc_start: 0.8198 (m-80) cc_final: 0.7595 (m-80) REVERT: C 1249 ASN cc_start: 0.8227 (p0) cc_final: 0.7896 (p0) REVERT: C 1328 ILE cc_start: 0.9030 (mt) cc_final: 0.8822 (mt) REVERT: D 214 ASP cc_start: 0.7810 (p0) cc_final: 0.7509 (p0) REVERT: D 259 MET cc_start: 0.7241 (tpp) cc_final: 0.6671 (tpp) REVERT: D 333 ARG cc_start: 0.6738 (mmm-85) cc_final: 0.5541 (tpt170) REVERT: D 425 ILE cc_start: 0.7691 (mm) cc_final: 0.7460 (mm) REVERT: D 491 ASN cc_start: 0.7883 (m110) cc_final: 0.7643 (m110) REVERT: D 504 ASP cc_start: 0.7464 (t70) cc_final: 0.6978 (t0) REVERT: D 537 LEU cc_start: 0.6547 (mt) cc_final: 0.6328 (mt) REVERT: D 547 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7241 (mm-30) REVERT: D 628 SER cc_start: 0.8447 (t) cc_final: 0.8168 (t) REVERT: D 629 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.6461 (ttp-110) REVERT: D 670 ASP cc_start: 0.7216 (m-30) cc_final: 0.6653 (p0) REVERT: D 706 TYR cc_start: 0.7845 (m-80) cc_final: 0.7564 (m-80) REVERT: D 802 GLN cc_start: 0.7585 (mt0) cc_final: 0.7057 (mm-40) REVERT: D 836 GLN cc_start: 0.8813 (mp10) cc_final: 0.8312 (mp10) REVERT: D 845 GLU cc_start: 0.7176 (tt0) cc_final: 0.6884 (tp30) REVERT: D 873 TYR cc_start: 0.7635 (m-80) cc_final: 0.7194 (m-80) REVERT: D 926 VAL cc_start: 0.8397 (t) cc_final: 0.8186 (m) REVERT: D 988 GLN cc_start: 0.8601 (tt0) cc_final: 0.8305 (mt0) REVERT: D 1038 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7870 (tt0) REVERT: D 1078 TYR cc_start: 0.7987 (t80) cc_final: 0.7591 (t80) REVERT: D 1093 PRO cc_start: 0.8538 (Cg_exo) cc_final: 0.7110 (Cg_endo) REVERT: D 1208 ASP cc_start: 0.7443 (t0) cc_final: 0.7182 (t0) REVERT: D 1226 ASP cc_start: 0.6970 (t0) cc_final: 0.6697 (t0) REVERT: D 1279 SER cc_start: 0.8153 (m) cc_final: 0.7789 (m) REVERT: D 1315 MET cc_start: 0.7982 (ttp) cc_final: 0.7636 (ttm) REVERT: E 243 GLN cc_start: 0.8024 (mt0) cc_final: 0.7421 (tp40) REVERT: E 438 ASN cc_start: 0.7776 (t0) cc_final: 0.7519 (m-40) REVERT: E 503 GLU cc_start: 0.6856 (tt0) cc_final: 0.6606 (tt0) REVERT: E 520 PHE cc_start: 0.7455 (m-10) cc_final: 0.6933 (m-10) REVERT: E 640 GLN cc_start: 0.6985 (mm-40) cc_final: 0.6354 (mt0) REVERT: E 641 ARG cc_start: 0.5629 (ptt90) cc_final: 0.5415 (ptt90) REVERT: E 975 SER cc_start: 0.8281 (p) cc_final: 0.8045 (p) REVERT: E 1210 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8120 (tt) REVERT: E 1265 MET cc_start: 0.8357 (mtm) cc_final: 0.8065 (mtm) REVERT: E 1275 ASP cc_start: 0.7720 (m-30) cc_final: 0.7463 (t0) REVERT: F 142 ASP cc_start: 0.7224 (t70) cc_final: 0.6650 (t70) REVERT: F 209 ASN cc_start: 0.8663 (t0) cc_final: 0.8308 (t0) REVERT: F 333 ARG cc_start: 0.7022 (mmm-85) cc_final: 0.6392 (mmt180) REVERT: F 438 ASN cc_start: 0.8238 (t0) cc_final: 0.7902 (t0) REVERT: F 447 ARG cc_start: 0.5044 (ptt180) cc_final: 0.4638 (ptt180) REVERT: F 561 ASN cc_start: 0.8610 (t0) cc_final: 0.8203 (t0) REVERT: F 640 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7612 (mt0) REVERT: F 800 LEU cc_start: 0.7182 (tp) cc_final: 0.6656 (tt) REVERT: F 953 ASP cc_start: 0.8082 (m-30) cc_final: 0.7378 (p0) REVERT: F 1318 GLU cc_start: 0.6922 (tt0) cc_final: 0.6674 (tt0) REVERT: G 293 ASN cc_start: 0.8593 (t0) cc_final: 0.8353 (t0) REVERT: G 313 ASP cc_start: 0.8625 (t0) cc_final: 0.8232 (t0) REVERT: G 398 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7982 (mpt180) REVERT: G 452 ASN cc_start: 0.6963 (m110) cc_final: 0.6604 (m110) REVERT: G 524 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7082 (tm-30) REVERT: G 536 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8087 (mp) REVERT: G 574 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7851 (mtmm) REVERT: G 623 ASN cc_start: 0.8184 (t0) cc_final: 0.7932 (t0) REVERT: G 688 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7882 (mm-30) REVERT: G 909 TYR cc_start: 0.7498 (t80) cc_final: 0.7297 (t80) REVERT: G 1014 MET cc_start: 0.7429 (mmm) cc_final: 0.7217 (mmm) REVERT: G 1038 GLU cc_start: 0.5860 (tt0) cc_final: 0.5628 (tt0) REVERT: G 1072 ASP cc_start: 0.6583 (p0) cc_final: 0.6153 (p0) REVERT: G 1144 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7904 (ttp-110) REVERT: G 1231 TYR cc_start: 0.7667 (m-80) cc_final: 0.7132 (m-80) REVERT: G 1313 ASP cc_start: 0.7801 (t70) cc_final: 0.7595 (t0) REVERT: G 1321 ASN cc_start: 0.8468 (m-40) cc_final: 0.8219 (m-40) outliers start: 244 outliers final: 140 residues processed: 1987 average time/residue: 0.5569 time to fit residues: 1932.3974 Evaluate side-chains 1668 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1521 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 1019 ILE Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1140 THR Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1247 ASN Chi-restraints excluded: chain C residue 1286 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 856 LEU Chi-restraints excluded: chain D residue 939 ASN Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1126 MET Chi-restraints excluded: chain D residue 1160 ILE Chi-restraints excluded: chain D residue 1162 SER Chi-restraints excluded: chain D residue 1170 ASP Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 494 GLU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 806 VAL Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1036 ASP Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1062 ILE Chi-restraints excluded: chain E residue 1118 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1308 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 699 THR Chi-restraints excluded: chain F residue 799 THR Chi-restraints excluded: chain F residue 804 LEU Chi-restraints excluded: chain F residue 886 SER Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 550 ILE Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 842 ASP Chi-restraints excluded: chain G residue 936 MET Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1108 SER Chi-restraints excluded: chain G residue 1142 ASN Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1308 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 581 optimal weight: 6.9990 chunk 475 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 699 optimal weight: 6.9990 chunk 755 optimal weight: 9.9990 chunk 623 optimal weight: 30.0000 chunk 693 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 561 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 HIS A 453 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 607 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A 696 HIS A 700 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 346 ASN B 459 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 320 GLN C 405 HIS C 428 GLN C 456 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 724 HIS C 864 HIS C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 493 HIS ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 933 ASN E 291 HIS E 293 ASN E 319 GLN E 369 ASN E 405 HIS ** E 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 GLN F 291 HIS ** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 HIS F 978 GLN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN G 640 GLN G1121 HIS G1234 GLN G1248 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 62651 Z= 0.404 Angle : 0.806 17.440 85237 Z= 0.407 Chirality : 0.049 0.227 9752 Planarity : 0.006 0.099 11061 Dihedral : 7.655 168.790 8714 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.66 % Favored : 93.24 % Rotamer: Outliers : 6.18 % Allowed : 15.46 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.18 % 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: -2.83 (0.09), residues: 7697 helix: -1.90 (0.09), residues: 2746 sheet: -2.14 (0.15), residues: 964 loop : -1.72 (0.09), residues: 3987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 742 HIS 0.021 0.002 HIS F1203 PHE 0.034 0.003 PHE B 159 TYR 0.038 0.002 TYR D1096 ARG 0.024 0.001 ARG C 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2329 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 1913 time to evaluate : 5.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7536 (m) cc_final: 0.7071 (m) REVERT: A 20 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7778 (ttp-170) REVERT: A 24 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7931 (mmtp) REVERT: A 53 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7491 (p) REVERT: A 91 ASP cc_start: 0.8710 (t0) cc_final: 0.8490 (t70) REVERT: A 116 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.3702 (p90) REVERT: A 137 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7971 (mm-40) REVERT: A 148 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 448 SER cc_start: 0.8058 (m) cc_final: 0.7122 (t) REVERT: A 475 LYS cc_start: 0.7286 (ptpp) cc_final: 0.6570 (pttt) REVERT: A 485 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7053 (pmt-80) REVERT: A 502 MET cc_start: 0.8428 (tpt) cc_final: 0.7912 (tpp) REVERT: A 539 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7115 (ttm110) REVERT: A 587 MET cc_start: 0.8374 (mtp) cc_final: 0.8159 (mtp) REVERT: A 626 ILE cc_start: 0.8302 (pt) cc_final: 0.8011 (pt) REVERT: A 758 MET cc_start: 0.7964 (tpp) cc_final: 0.7634 (tmm) REVERT: A 828 MET cc_start: 0.7062 (ppp) cc_final: 0.6770 (tmm) REVERT: A 830 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6852 (mp) REVERT: A 845 TYR cc_start: 0.7456 (t80) cc_final: 0.7142 (t80) REVERT: A 854 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6979 (p0) REVERT: A 857 PHE cc_start: 0.8463 (m-10) cc_final: 0.8175 (m-10) REVERT: A 860 ASP cc_start: 0.7955 (p0) cc_final: 0.7328 (t0) REVERT: A 883 GLU cc_start: 0.7754 (tp30) cc_final: 0.7107 (mm-30) REVERT: A 889 SER cc_start: 0.8730 (m) cc_final: 0.8426 (p) REVERT: A 919 GLU cc_start: 0.7814 (tp30) cc_final: 0.7486 (tp30) REVERT: A 922 LYS cc_start: 0.7792 (tptp) cc_final: 0.7337 (mmtp) REVERT: A 966 ASP cc_start: 0.8366 (t70) cc_final: 0.8152 (t70) REVERT: A 1000 ASP cc_start: 0.8176 (t0) cc_final: 0.7543 (m-30) REVERT: A 1085 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6359 (mtpt) REVERT: A 1094 LYS cc_start: 0.6751 (mmtp) cc_final: 0.6396 (mmtm) REVERT: A 1103 ASP cc_start: 0.8395 (t0) cc_final: 0.8111 (t0) REVERT: B 146 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 204 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: B 277 ASP cc_start: 0.8352 (m-30) cc_final: 0.7861 (m-30) REVERT: B 280 LEU cc_start: 0.8054 (pp) cc_final: 0.7825 (pp) REVERT: B 289 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 317 SER cc_start: 0.8630 (m) cc_final: 0.8395 (p) REVERT: B 321 MET cc_start: 0.8874 (mtp) cc_final: 0.8570 (mtp) REVERT: B 407 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 444 LYS cc_start: 0.7998 (tttm) cc_final: 0.7787 (ttmm) REVERT: B 466 HIS cc_start: 0.7835 (m90) cc_final: 0.7246 (m90) REVERT: B 503 THR cc_start: 0.8654 (m) cc_final: 0.8307 (p) REVERT: C 123 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7360 (mm-30) REVERT: C 135 LYS cc_start: 0.3592 (pptt) cc_final: 0.3373 (mttm) REVERT: C 153 ASP cc_start: 0.7202 (t70) cc_final: 0.6902 (t70) REVERT: C 168 VAL cc_start: 0.8460 (t) cc_final: 0.8224 (p) REVERT: C 174 PHE cc_start: 0.8101 (m-80) cc_final: 0.7546 (m-80) REVERT: C 274 MET cc_start: 0.2465 (mmt) cc_final: 0.1548 (mmt) REVERT: C 317 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7274 (mtp) REVERT: C 361 ASN cc_start: 0.8702 (m-40) cc_final: 0.8365 (m-40) REVERT: C 366 MET cc_start: 0.8119 (mmm) cc_final: 0.7777 (mmm) REVERT: C 377 LYS cc_start: 0.9241 (mttt) cc_final: 0.8631 (mtpt) REVERT: C 419 TYR cc_start: 0.8613 (m-80) cc_final: 0.8345 (m-10) REVERT: C 438 ASN cc_start: 0.8791 (t0) cc_final: 0.8443 (t0) REVERT: C 491 ASN cc_start: 0.8535 (m110) cc_final: 0.8065 (t0) REVERT: C 494 GLU cc_start: 0.7574 (pt0) cc_final: 0.7312 (pt0) REVERT: C 504 ASP cc_start: 0.7947 (t70) cc_final: 0.7741 (t0) REVERT: C 588 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9177 (mt) REVERT: C 629 ARG cc_start: 0.7317 (mmm-85) cc_final: 0.6019 (ttt-90) REVERT: C 646 ASN cc_start: 0.8292 (t0) cc_final: 0.7924 (t0) REVERT: C 723 ASN cc_start: 0.8115 (m110) cc_final: 0.7825 (m-40) REVERT: C 759 ASP cc_start: 0.8331 (t0) cc_final: 0.7742 (t0) REVERT: C 844 ASP cc_start: 0.8474 (t70) cc_final: 0.8023 (p0) REVERT: C 849 MET cc_start: 0.7889 (ttp) cc_final: 0.7651 (ttp) REVERT: C 860 ARG cc_start: 0.8711 (tmt90) cc_final: 0.8495 (ttt180) REVERT: C 898 GLN cc_start: 0.8230 (tt0) cc_final: 0.7994 (tp40) REVERT: C 1038 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7286 (tt0) REVERT: C 1048 ASP cc_start: 0.7617 (m-30) cc_final: 0.7406 (m-30) REVERT: C 1085 ASP cc_start: 0.7705 (p0) cc_final: 0.7479 (p0) REVERT: C 1226 ASP cc_start: 0.8170 (t0) cc_final: 0.7775 (t0) REVERT: D 173 GLN cc_start: 0.8290 (pt0) cc_final: 0.7987 (pt0) REVERT: D 259 MET cc_start: 0.8212 (tpp) cc_final: 0.7858 (tpp) REVERT: D 274 MET cc_start: 0.7371 (tpp) cc_final: 0.6977 (ttm) REVERT: D 333 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.6285 (tpt170) REVERT: D 406 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7875 (p0) REVERT: D 574 LYS cc_start: 0.8208 (mtpm) cc_final: 0.7884 (mtmm) REVERT: D 637 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7954 (p90) REVERT: D 646 ASN cc_start: 0.8479 (t0) cc_final: 0.8069 (t0) REVERT: D 673 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7069 (mt0) REVERT: D 698 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8561 (m-70) REVERT: D 728 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9033 (mmtp) REVERT: D 747 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7910 (ptm160) REVERT: D 808 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7740 (mm110) REVERT: D 812 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7046 (mmtt) REVERT: D 956 ASP cc_start: 0.7759 (m-30) cc_final: 0.7152 (m-30) REVERT: D 988 GLN cc_start: 0.8886 (tt0) cc_final: 0.8665 (tt0) REVERT: D 1014 MET cc_start: 0.8206 (tpp) cc_final: 0.7373 (tpp) REVERT: D 1130 SER cc_start: 0.8623 (t) cc_final: 0.8391 (m) REVERT: D 1140 THR cc_start: 0.8590 (m) cc_final: 0.8000 (p) REVERT: D 1315 MET cc_start: 0.8109 (ttp) cc_final: 0.7866 (ttm) REVERT: D 1326 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8747 (mtp180) REVERT: E 137 ILE cc_start: 0.8844 (mm) cc_final: 0.8618 (tt) REVERT: E 243 GLN cc_start: 0.8278 (mt0) cc_final: 0.8044 (mt0) REVERT: E 370 VAL cc_start: 0.9123 (m) cc_final: 0.8905 (p) REVERT: E 788 MET cc_start: 0.0232 (tpp) cc_final: -0.0931 (tpt) REVERT: E 812 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8175 (mttt) REVERT: E 822 MET cc_start: 0.8852 (tmm) cc_final: 0.8533 (tmm) REVERT: E 898 GLN cc_start: 0.8518 (tt0) cc_final: 0.8258 (tt0) REVERT: E 914 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7573 (mm-30) REVERT: E 957 PHE cc_start: 0.8941 (t80) cc_final: 0.8694 (t80) REVERT: E 1032 ASP cc_start: 0.7613 (t0) cc_final: 0.7341 (t0) REVERT: E 1055 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8282 (tp) REVERT: E 1064 ASN cc_start: 0.8467 (t0) cc_final: 0.8216 (t0) REVERT: E 1076 ILE cc_start: 0.8990 (mm) cc_final: 0.8627 (mm) REVERT: E 1077 MET cc_start: 0.7555 (ttt) cc_final: 0.7324 (ttm) REVERT: E 1227 MET cc_start: 0.8212 (mmt) cc_final: 0.7462 (ptt) REVERT: E 1264 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7706 (mp0) REVERT: E 1265 MET cc_start: 0.8556 (mtm) cc_final: 0.8215 (mtm) REVERT: E 1279 SER cc_start: 0.8585 (m) cc_final: 0.8329 (m) REVERT: F 142 ASP cc_start: 0.7550 (t70) cc_final: 0.6242 (t70) REVERT: F 146 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7522 (mt-10) REVERT: F 242 GLU cc_start: 0.7869 (pm20) cc_final: 0.7624 (pm20) REVERT: F 276 ASN cc_start: 0.8748 (p0) cc_final: 0.8508 (p0) REVERT: F 333 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.6580 (tpt170) REVERT: F 422 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8721 (tt) REVERT: F 438 ASN cc_start: 0.8909 (t0) cc_final: 0.8643 (t0) REVERT: F 441 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7767 (ttm110) REVERT: F 447 ARG cc_start: 0.6591 (ptt180) cc_final: 0.6366 (ptt180) REVERT: F 501 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.9182 (t) REVERT: F 561 ASN cc_start: 0.8669 (t0) cc_final: 0.8363 (t0) REVERT: F 637 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8386 (p90) REVERT: F 640 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8216 (mm-40) REVERT: F 746 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: F 788 MET cc_start: 0.0052 (mmm) cc_final: -0.0216 (mmm) REVERT: F 856 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8606 (mm) REVERT: F 861 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7774 (mm-30) REVERT: F 899 SER cc_start: 0.8364 (p) cc_final: 0.8106 (t) REVERT: F 909 TYR cc_start: 0.8163 (t80) cc_final: 0.7915 (t80) REVERT: F 941 TYR cc_start: 0.8789 (p90) cc_final: 0.8297 (p90) REVERT: F 973 THR cc_start: 0.8607 (m) cc_final: 0.8364 (p) REVERT: F 1030 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8445 (mtm-85) REVERT: F 1038 GLU cc_start: 0.6375 (tt0) cc_final: 0.6054 (tt0) REVERT: F 1083 ASP cc_start: 0.8754 (t0) cc_final: 0.8392 (t70) REVERT: F 1174 THR cc_start: 0.8742 (p) cc_final: 0.8463 (p) REVERT: F 1278 TYR cc_start: 0.8594 (m-80) cc_final: 0.8281 (m-10) REVERT: F 1279 SER cc_start: 0.8160 (m) cc_final: 0.7921 (m) REVERT: F 1292 GLU cc_start: 0.7524 (tt0) cc_final: 0.7121 (tt0) REVERT: F 1318 GLU cc_start: 0.7279 (tt0) cc_final: 0.6711 (tt0) REVERT: G 186 ASP cc_start: 0.8503 (m-30) cc_final: 0.8244 (m-30) REVERT: G 243 GLN cc_start: 0.7944 (mt0) cc_final: 0.7556 (tp-100) REVERT: G 283 ASN cc_start: 0.8597 (t0) cc_final: 0.8352 (t0) REVERT: G 290 TYR cc_start: 0.7998 (p90) cc_final: 0.7789 (p90) REVERT: G 335 ASP cc_start: 0.8308 (t0) cc_final: 0.7900 (t70) REVERT: G 438 ASN cc_start: 0.8703 (t0) cc_final: 0.8297 (t0) REVERT: G 452 ASN cc_start: 0.7410 (m110) cc_final: 0.7044 (m110) REVERT: G 620 ILE cc_start: 0.9189 (mm) cc_final: 0.8924 (mt) REVERT: G 623 ASN cc_start: 0.8390 (t0) cc_final: 0.7988 (t0) REVERT: G 671 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8158 (p0) REVERT: G 682 GLN cc_start: 0.8457 (mt0) cc_final: 0.8231 (mt0) REVERT: G 746 GLU cc_start: 0.6876 (tt0) cc_final: 0.6378 (tt0) REVERT: G 838 GLU cc_start: 0.7669 (mp0) cc_final: 0.7335 (pt0) REVERT: G 841 ASP cc_start: 0.6450 (m-30) cc_final: 0.6147 (m-30) REVERT: G 976 THR cc_start: 0.8456 (p) cc_final: 0.8207 (t) REVERT: G 1038 GLU cc_start: 0.5624 (tt0) cc_final: 0.5245 (mp0) REVERT: G 1061 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8761 (tp) REVERT: G 1130 SER cc_start: 0.8569 (t) cc_final: 0.8368 (p) REVERT: G 1144 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8422 (ttp-110) REVERT: G 1182 GLU cc_start: 0.8127 (tt0) cc_final: 0.7818 (tp30) outliers start: 416 outliers final: 238 residues processed: 2170 average time/residue: 0.5409 time to fit residues: 2022.6323 Evaluate side-chains 1753 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1494 time to evaluate : 5.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1085 LYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 825 SER Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 864 HIS Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1019 ILE Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1080 THR Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1140 THR Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1179 THR Chi-restraints excluded: chain C residue 1189 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1126 MET Chi-restraints excluded: chain D residue 1170 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1294 ASP Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 578 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 766 ILE Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 806 VAL Chi-restraints excluded: chain E residue 814 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1030 ARG Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1052 LEU Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 665 GLU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 746 GLU Chi-restraints excluded: chain F residue 766 ILE Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 856 LEU Chi-restraints excluded: chain F residue 890 THR Chi-restraints excluded: chain F residue 925 VAL Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1118 THR Chi-restraints excluded: chain F residue 1301 VAL Chi-restraints excluded: chain F residue 1308 ASN Chi-restraints excluded: chain F residue 1313 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 559 THR Chi-restraints excluded: chain G residue 560 ILE Chi-restraints excluded: chain G residue 582 SER Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 718 ASN Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain G residue 823 ILE Chi-restraints excluded: chain G residue 842 ASP Chi-restraints excluded: chain G residue 849 MET Chi-restraints excluded: chain G residue 850 THR Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 894 VAL Chi-restraints excluded: chain G residue 961 SER Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1061 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1108 SER Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1227 MET Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1301 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 7.9990 chunk 525 optimal weight: 7.9990 chunk 363 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 469 optimal weight: 5.9990 chunk 702 optimal weight: 6.9990 chunk 743 optimal weight: 0.9990 chunk 366 optimal weight: 6.9990 chunk 665 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN A1154 ASN B 9 HIS B 59 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN C 693 ASN ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 GLN D1015 GLN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 ASN F 243 GLN F 291 HIS F 407 HIS ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 HIS ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 802 GLN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 GLN ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 GLN ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 981 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 62651 Z= 0.241 Angle : 0.665 17.304 85237 Z= 0.329 Chirality : 0.045 0.224 9752 Planarity : 0.004 0.072 11061 Dihedral : 7.180 168.606 8708 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.07 % Favored : 94.83 % Rotamer: Outliers : 5.41 % Allowed : 19.83 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % 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: -2.35 (0.09), residues: 7697 helix: -1.38 (0.09), residues: 2755 sheet: -1.99 (0.15), residues: 956 loop : -1.50 (0.10), residues: 3986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 764 HIS 0.019 0.001 HIS C 864 PHE 0.025 0.002 PHE B 159 TYR 0.020 0.001 TYR A1083 ARG 0.006 0.000 ARG F 911 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1979 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1615 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7649 (pm20) cc_final: 0.7384 (pm20) REVERT: A 24 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7903 (mmtp) REVERT: A 37 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.1524 (mtp180) REVERT: A 53 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7101 (p) REVERT: A 116 TYR cc_start: 0.4658 (OUTLIER) cc_final: 0.3947 (p90) REVERT: A 139 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7439 (mtpp) REVERT: A 434 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7011 (pt0) REVERT: A 475 LYS cc_start: 0.7046 (ptpp) cc_final: 0.6659 (pttt) REVERT: A 484 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7308 (ttt180) REVERT: A 485 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7295 (pmt-80) REVERT: A 502 MET cc_start: 0.8294 (tpt) cc_final: 0.7882 (tpp) REVERT: A 513 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 539 ARG cc_start: 0.7758 (ptp-170) cc_final: 0.7295 (ttm110) REVERT: A 587 MET cc_start: 0.8376 (mtp) cc_final: 0.8020 (mtp) REVERT: A 626 ILE cc_start: 0.8207 (pt) cc_final: 0.7943 (pt) REVERT: A 634 GLU cc_start: 0.8223 (pp20) cc_final: 0.7629 (pp20) REVERT: A 758 MET cc_start: 0.8165 (tpp) cc_final: 0.7817 (tmm) REVERT: A 828 MET cc_start: 0.7096 (ppp) cc_final: 0.6746 (tmm) REVERT: A 845 TYR cc_start: 0.7292 (t80) cc_final: 0.6989 (t80) REVERT: A 857 PHE cc_start: 0.8637 (m-10) cc_final: 0.8433 (m-10) REVERT: A 860 ASP cc_start: 0.7943 (p0) cc_final: 0.7299 (t0) REVERT: A 875 LEU cc_start: 0.8021 (tt) cc_final: 0.7772 (tt) REVERT: A 919 GLU cc_start: 0.7577 (tp30) cc_final: 0.7275 (tp30) REVERT: A 922 LYS cc_start: 0.7726 (tptp) cc_final: 0.7270 (mmtp) REVERT: A 1000 ASP cc_start: 0.8260 (t0) cc_final: 0.7744 (m-30) REVERT: A 1094 LYS cc_start: 0.6610 (mmtp) cc_final: 0.6228 (mmtm) REVERT: A 1139 TYR cc_start: 0.8518 (t80) cc_final: 0.7568 (t80) REVERT: A 1144 SER cc_start: 0.8366 (m) cc_final: 0.7974 (t) REVERT: A 1153 ASP cc_start: 0.8000 (t0) cc_final: 0.7770 (t0) REVERT: A 1174 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7774 (t) REVERT: B 146 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7849 (mm-30) REVERT: B 193 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: B 204 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7973 (ttp-110) REVERT: B 277 ASP cc_start: 0.8363 (m-30) cc_final: 0.7904 (m-30) REVERT: B 288 LYS cc_start: 0.8702 (tttt) cc_final: 0.7815 (ttmm) REVERT: B 289 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 314 MET cc_start: 0.8735 (mtp) cc_final: 0.8501 (mtp) REVERT: B 321 MET cc_start: 0.8828 (mtp) cc_final: 0.8505 (mtp) REVERT: B 451 GLU cc_start: 0.8531 (tt0) cc_final: 0.8298 (tt0) REVERT: B 466 HIS cc_start: 0.7800 (m90) cc_final: 0.7238 (m90) REVERT: B 503 THR cc_start: 0.8618 (m) cc_final: 0.8244 (p) REVERT: C 123 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 135 LYS cc_start: 0.3988 (pptt) cc_final: 0.3416 (mttm) REVERT: C 173 GLN cc_start: 0.8370 (tt0) cc_final: 0.8057 (tt0) REVERT: C 174 PHE cc_start: 0.7972 (m-80) cc_final: 0.7171 (m-80) REVERT: C 187 ASP cc_start: 0.7457 (t70) cc_final: 0.6982 (t70) REVERT: C 274 MET cc_start: 0.1829 (mmt) cc_final: 0.1224 (mmt) REVERT: C 361 ASN cc_start: 0.8761 (m-40) cc_final: 0.8400 (m-40) REVERT: C 377 LYS cc_start: 0.9289 (mttt) cc_final: 0.8624 (mtpt) REVERT: C 419 TYR cc_start: 0.8655 (m-80) cc_final: 0.8447 (m-10) REVERT: C 429 ILE cc_start: 0.8929 (mt) cc_final: 0.8707 (mp) REVERT: C 438 ASN cc_start: 0.8775 (t0) cc_final: 0.8445 (t0) REVERT: C 471 SER cc_start: 0.8934 (p) cc_final: 0.8612 (p) REVERT: C 491 ASN cc_start: 0.8593 (m110) cc_final: 0.8012 (t0) REVERT: C 492 VAL cc_start: 0.9225 (t) cc_final: 0.8854 (t) REVERT: C 500 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 544 TYR cc_start: 0.8414 (m-80) cc_final: 0.8082 (m-80) REVERT: C 629 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.5831 (ttp80) REVERT: C 646 ASN cc_start: 0.8199 (t0) cc_final: 0.7866 (t0) REVERT: C 723 ASN cc_start: 0.8018 (m110) cc_final: 0.7801 (m-40) REVERT: C 727 PHE cc_start: 0.8997 (t80) cc_final: 0.8601 (t80) REVERT: C 759 ASP cc_start: 0.8243 (t0) cc_final: 0.7910 (t0) REVERT: C 1038 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 1048 ASP cc_start: 0.7621 (m-30) cc_final: 0.7404 (m-30) REVERT: C 1170 ASP cc_start: 0.8098 (t0) cc_final: 0.7532 (t0) REVERT: C 1308 ASN cc_start: 0.8726 (t0) cc_final: 0.8467 (t0) REVERT: C 1313 ASP cc_start: 0.8685 (p0) cc_final: 0.8456 (p0) REVERT: C 1324 ASP cc_start: 0.8696 (t0) cc_final: 0.8471 (t70) REVERT: D 259 MET cc_start: 0.8182 (tpp) cc_final: 0.7675 (tpp) REVERT: D 274 MET cc_start: 0.7285 (tpp) cc_final: 0.7047 (ttm) REVERT: D 276 ASN cc_start: 0.8586 (p0) cc_final: 0.8255 (p0) REVERT: D 333 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.6303 (tpt170) REVERT: D 500 GLU cc_start: 0.6735 (tp30) cc_final: 0.6505 (tp30) REVERT: D 501 SER cc_start: 0.8634 (p) cc_final: 0.8206 (p) REVERT: D 526 ASN cc_start: 0.9021 (t0) cc_final: 0.8650 (t0) REVERT: D 548 TYR cc_start: 0.8232 (t80) cc_final: 0.7946 (t80) REVERT: D 574 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7997 (mtmm) REVERT: D 637 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7921 (p90) REVERT: D 646 ASN cc_start: 0.8393 (t0) cc_final: 0.7916 (t0) REVERT: D 670 ASP cc_start: 0.7626 (m-30) cc_final: 0.6750 (t0) REVERT: D 673 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7495 (mt0) REVERT: D 698 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8348 (m-70) REVERT: D 728 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8992 (mmtp) REVERT: D 765 PRO cc_start: 0.8862 (Cg_exo) cc_final: 0.8611 (Cg_endo) REVERT: D 808 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7669 (mm110) REVERT: D 812 LYS cc_start: 0.7611 (mtpt) cc_final: 0.7157 (mmtt) REVERT: D 921 ASP cc_start: 0.8114 (p0) cc_final: 0.7713 (p0) REVERT: D 935 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7974 (mm110) REVERT: D 956 ASP cc_start: 0.7753 (m-30) cc_final: 0.7429 (m-30) REVERT: D 988 GLN cc_start: 0.8808 (tt0) cc_final: 0.8590 (tt0) REVERT: D 1014 MET cc_start: 0.7847 (tpp) cc_final: 0.7257 (tpp) REVERT: D 1097 VAL cc_start: 0.8568 (t) cc_final: 0.8174 (m) REVERT: D 1130 SER cc_start: 0.8565 (t) cc_final: 0.8327 (m) REVERT: D 1140 THR cc_start: 0.8719 (m) cc_final: 0.8143 (p) REVERT: D 1255 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7330 (ttp-110) REVERT: E 137 ILE cc_start: 0.8865 (mm) cc_final: 0.8627 (tt) REVERT: E 457 GLN cc_start: 0.8252 (tt0) cc_final: 0.7427 (tp40) REVERT: E 728 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: E 788 MET cc_start: 0.0628 (tpp) cc_final: 0.0331 (tpp) REVERT: E 812 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8155 (mttt) REVERT: E 898 GLN cc_start: 0.8579 (tt0) cc_final: 0.8334 (tt0) REVERT: E 914 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7594 (mm-30) REVERT: E 1055 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 1064 ASN cc_start: 0.8532 (t0) cc_final: 0.8152 (t0) REVERT: E 1076 ILE cc_start: 0.8971 (mm) cc_final: 0.8597 (mm) REVERT: E 1077 MET cc_start: 0.7692 (ttt) cc_final: 0.7437 (ttm) REVERT: E 1227 MET cc_start: 0.8138 (mmt) cc_final: 0.7435 (ptt) REVERT: E 1264 GLU cc_start: 0.8677 (mt-10) cc_final: 0.7791 (mp0) REVERT: E 1265 MET cc_start: 0.8553 (mtm) cc_final: 0.8206 (mtm) REVERT: E 1279 SER cc_start: 0.8473 (m) cc_final: 0.8177 (m) REVERT: F 142 ASP cc_start: 0.7708 (t70) cc_final: 0.6208 (t70) REVERT: F 290 TYR cc_start: 0.8467 (p90) cc_final: 0.8124 (p90) REVERT: F 333 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.6603 (tpt170) REVERT: F 366 MET cc_start: 0.8731 (mmm) cc_final: 0.8459 (mmm) REVERT: F 422 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8721 (tt) REVERT: F 438 ASN cc_start: 0.8863 (t0) cc_final: 0.8562 (t0) REVERT: F 441 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7720 (ttm110) REVERT: F 561 ASN cc_start: 0.8745 (t0) cc_final: 0.8504 (t0) REVERT: F 637 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8429 (p90) REVERT: F 759 ASP cc_start: 0.8520 (t0) cc_final: 0.8131 (t70) REVERT: F 788 MET cc_start: 0.0457 (mmm) cc_final: 0.0257 (mmm) REVERT: F 856 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8512 (mm) REVERT: F 899 SER cc_start: 0.8339 (p) cc_final: 0.8130 (t) REVERT: F 1031 TYR cc_start: 0.8822 (t80) cc_final: 0.8101 (t80) REVERT: F 1038 GLU cc_start: 0.6207 (tt0) cc_final: 0.5968 (tt0) REVERT: F 1279 SER cc_start: 0.8110 (m) cc_final: 0.7874 (m) REVERT: F 1318 GLU cc_start: 0.7348 (tt0) cc_final: 0.6726 (tt0) REVERT: G 186 ASP cc_start: 0.8518 (m-30) cc_final: 0.8247 (m-30) REVERT: G 230 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7652 (t70) REVERT: G 318 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8496 (mp) REVERT: G 324 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7648 (mmtt) REVERT: G 335 ASP cc_start: 0.8330 (t0) cc_final: 0.7964 (t70) REVERT: G 339 LEU cc_start: 0.9065 (mp) cc_final: 0.8817 (mt) REVERT: G 438 ASN cc_start: 0.8716 (t0) cc_final: 0.8234 (t0) REVERT: G 452 ASN cc_start: 0.7522 (m110) cc_final: 0.7195 (m110) REVERT: G 620 ILE cc_start: 0.9184 (mm) cc_final: 0.8912 (mt) REVERT: G 623 ASN cc_start: 0.8344 (t0) cc_final: 0.7883 (t0) REVERT: G 671 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8125 (p0) REVERT: G 682 GLN cc_start: 0.8486 (mt0) cc_final: 0.8174 (mt0) REVERT: G 709 MET cc_start: 0.8959 (ttm) cc_final: 0.8577 (mtp) REVERT: G 746 GLU cc_start: 0.6921 (tt0) cc_final: 0.6398 (tt0) REVERT: G 838 GLU cc_start: 0.7647 (mp0) cc_final: 0.7040 (pt0) REVERT: G 942 HIS cc_start: 0.8469 (t-170) cc_final: 0.8225 (t-170) REVERT: G 1003 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7091 (ptp90) REVERT: G 1038 GLU cc_start: 0.5580 (tt0) cc_final: 0.5227 (mp0) REVERT: G 1061 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8765 (tp) REVERT: G 1118 THR cc_start: 0.8894 (t) cc_final: 0.8637 (t) REVERT: G 1144 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8469 (ttp-110) REVERT: G 1182 GLU cc_start: 0.8099 (tt0) cc_final: 0.7866 (tp30) REVERT: G 1194 MET cc_start: 0.9070 (mmt) cc_final: 0.8718 (mmm) REVERT: G 1207 MET cc_start: 0.8051 (ppp) cc_final: 0.7663 (tmm) REVERT: G 1240 ARG cc_start: 0.8217 (ptm-80) cc_final: 0.7959 (mtm180) REVERT: G 1315 MET cc_start: 0.8499 (ppp) cc_final: 0.8252 (ppp) outliers start: 364 outliers final: 238 residues processed: 1830 average time/residue: 0.5407 time to fit residues: 1713.5601 Evaluate side-chains 1733 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1473 time to evaluate : 5.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1110 PHE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1140 THR Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1179 THR Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1286 VAL Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1314 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 503 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 948 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1085 ASP Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain D residue 1294 ASP Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1306 THR Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 491 ASN Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 698 HIS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain E residue 766 ILE Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 814 THR Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 933 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1223 SER Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 643 THR Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 766 ILE Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 856 LEU Chi-restraints excluded: chain F residue 886 SER Chi-restraints excluded: chain F residue 925 VAL Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1195 THR Chi-restraints excluded: chain F residue 1269 THR Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 400 GLU Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 698 HIS Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 849 MET Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 948 ILE Chi-restraints excluded: chain G residue 961 SER Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1043 SER Chi-restraints excluded: chain G residue 1061 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1108 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1142 ASN Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1227 MET Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1275 ASP Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 8.9990 chunk 421 optimal weight: 0.4980 chunk 10 optimal weight: 20.0000 chunk 553 optimal weight: 8.9990 chunk 306 optimal weight: 7.9990 chunk 634 optimal weight: 0.3980 chunk 513 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 667 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 748 GLN C1018 GLN ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 ASN D 173 GLN D1154 ASN D1321 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 GLN F 283 ASN F 452 ASN F 577 GLN ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 GLN G 533 GLN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62651 Z= 0.185 Angle : 0.632 17.154 85237 Z= 0.309 Chirality : 0.044 0.300 9752 Planarity : 0.004 0.072 11061 Dihedral : 6.754 168.698 8702 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 5.24 % Allowed : 21.12 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.10 % 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: -1.94 (0.09), residues: 7697 helix: -0.90 (0.10), residues: 2767 sheet: -1.87 (0.15), residues: 984 loop : -1.33 (0.10), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 764 HIS 0.007 0.001 HIS C 382 PHE 0.023 0.001 PHE B 159 TYR 0.015 0.001 TYR F 419 ARG 0.009 0.000 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 1605 time to evaluate : 5.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7802 (mmtp) REVERT: A 92 GLU cc_start: 0.7956 (mp0) cc_final: 0.7087 (tm-30) REVERT: A 116 TYR cc_start: 0.4629 (OUTLIER) cc_final: 0.4005 (p90) REVERT: A 226 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: A 434 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6846 (pt0) REVERT: A 475 LYS cc_start: 0.7110 (ptpp) cc_final: 0.6688 (mttt) REVERT: A 485 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7317 (pmt-80) REVERT: A 502 MET cc_start: 0.8235 (tpt) cc_final: 0.7705 (tpp) REVERT: A 513 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 539 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7466 (ttm110) REVERT: A 587 MET cc_start: 0.8040 (mtp) cc_final: 0.7717 (mtp) REVERT: A 626 ILE cc_start: 0.8269 (pt) cc_final: 0.8050 (pt) REVERT: A 634 GLU cc_start: 0.8204 (pp20) cc_final: 0.7591 (pp20) REVERT: A 744 ARG cc_start: 0.8401 (ttm170) cc_final: 0.7843 (ttm170) REVERT: A 758 MET cc_start: 0.8005 (tpp) cc_final: 0.7500 (tmm) REVERT: A 828 MET cc_start: 0.7226 (ppp) cc_final: 0.6751 (tmm) REVERT: A 845 TYR cc_start: 0.7436 (t80) cc_final: 0.7167 (t80) REVERT: A 860 ASP cc_start: 0.8007 (p0) cc_final: 0.7291 (t0) REVERT: A 883 GLU cc_start: 0.7540 (tp30) cc_final: 0.7163 (mp0) REVERT: A 884 MET cc_start: 0.8709 (ttp) cc_final: 0.8391 (ttt) REVERT: A 922 LYS cc_start: 0.7642 (tptp) cc_final: 0.7379 (tppt) REVERT: A 936 SER cc_start: 0.8365 (m) cc_final: 0.7942 (p) REVERT: A 1000 ASP cc_start: 0.8183 (t0) cc_final: 0.7616 (m-30) REVERT: A 1094 LYS cc_start: 0.6584 (mmtp) cc_final: 0.6219 (mmtm) REVERT: A 1103 ASP cc_start: 0.8251 (t0) cc_final: 0.7694 (t0) REVERT: A 1139 TYR cc_start: 0.8528 (t80) cc_final: 0.7561 (t80) REVERT: A 1144 SER cc_start: 0.8446 (m) cc_final: 0.8054 (t) REVERT: A 1156 VAL cc_start: 0.9001 (t) cc_final: 0.8776 (p) REVERT: A 1174 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 1196 LYS cc_start: 0.8625 (mptt) cc_final: 0.8397 (mmtp) REVERT: A 1202 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8887 (mp) REVERT: B 76 MET cc_start: 0.7514 (tpp) cc_final: 0.7303 (mtt) REVERT: B 146 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 154 LEU cc_start: 0.7166 (mt) cc_final: 0.6790 (mp) REVERT: B 204 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7930 (ttp-110) REVERT: B 277 ASP cc_start: 0.8377 (m-30) cc_final: 0.7940 (m-30) REVERT: B 288 LYS cc_start: 0.8473 (tttt) cc_final: 0.7617 (ttmm) REVERT: B 314 MET cc_start: 0.8784 (mtp) cc_final: 0.8544 (mtp) REVERT: B 321 MET cc_start: 0.8715 (mtp) cc_final: 0.8360 (mtp) REVERT: B 407 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (mm) REVERT: B 451 GLU cc_start: 0.8604 (tt0) cc_final: 0.8371 (tt0) REVERT: B 503 THR cc_start: 0.8598 (m) cc_final: 0.8340 (p) REVERT: C 123 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 135 LYS cc_start: 0.4747 (pptt) cc_final: 0.3829 (mttm) REVERT: C 173 GLN cc_start: 0.8366 (tt0) cc_final: 0.8082 (tt0) REVERT: C 174 PHE cc_start: 0.7988 (m-80) cc_final: 0.7199 (m-80) REVERT: C 223 LYS cc_start: 0.8753 (mttp) cc_final: 0.8437 (mmmm) REVERT: C 312 ARG cc_start: 0.8635 (tmm-80) cc_final: 0.8358 (tmm-80) REVERT: C 313 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8502 (t70) REVERT: C 361 ASN cc_start: 0.8773 (m-40) cc_final: 0.8458 (m-40) REVERT: C 377 LYS cc_start: 0.9168 (mttt) cc_final: 0.8534 (mtpt) REVERT: C 429 ILE cc_start: 0.8941 (mt) cc_final: 0.8713 (mp) REVERT: C 471 SER cc_start: 0.8905 (p) cc_final: 0.8594 (p) REVERT: C 491 ASN cc_start: 0.8557 (m110) cc_final: 0.8023 (t0) REVERT: C 492 VAL cc_start: 0.9245 (t) cc_final: 0.8973 (t) REVERT: C 544 TYR cc_start: 0.8302 (m-80) cc_final: 0.8102 (m-80) REVERT: C 576 ASP cc_start: 0.8004 (t0) cc_final: 0.7714 (t70) REVERT: C 629 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.5872 (ttt-90) REVERT: C 661 ASN cc_start: 0.8161 (t0) cc_final: 0.7870 (t0) REVERT: C 723 ASN cc_start: 0.7905 (m110) cc_final: 0.7643 (m-40) REVERT: C 727 PHE cc_start: 0.8962 (t80) cc_final: 0.8628 (t80) REVERT: C 759 ASP cc_start: 0.8302 (t0) cc_final: 0.8072 (t0) REVERT: C 783 ASP cc_start: 0.5309 (OUTLIER) cc_final: 0.4522 (p0) REVERT: C 1014 MET cc_start: 0.7271 (tpp) cc_final: 0.7043 (tpp) REVERT: C 1037 ILE cc_start: 0.9117 (mp) cc_final: 0.8898 (mp) REVERT: C 1038 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 1041 ARG cc_start: 0.8684 (tpt-90) cc_final: 0.8483 (tpt-90) REVERT: C 1104 ARG cc_start: 0.8369 (ttt90) cc_final: 0.7914 (ptm-80) REVERT: C 1139 MET cc_start: 0.8540 (tpp) cc_final: 0.8143 (ttm) REVERT: C 1170 ASP cc_start: 0.8093 (t0) cc_final: 0.7561 (t0) REVERT: C 1225 GLU cc_start: 0.4556 (tp30) cc_final: 0.3825 (tt0) REVERT: C 1308 ASN cc_start: 0.8711 (t0) cc_final: 0.8445 (t0) REVERT: C 1324 ASP cc_start: 0.8755 (t0) cc_final: 0.8511 (t70) REVERT: D 259 MET cc_start: 0.8146 (tpp) cc_final: 0.7752 (tpp) REVERT: D 276 ASN cc_start: 0.8631 (p0) cc_final: 0.8331 (p0) REVERT: D 333 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.6348 (tpt170) REVERT: D 491 ASN cc_start: 0.8401 (m110) cc_final: 0.8108 (m110) REVERT: D 500 GLU cc_start: 0.6734 (tp30) cc_final: 0.6526 (tp30) REVERT: D 537 LEU cc_start: 0.7690 (mt) cc_final: 0.7482 (mt) REVERT: D 548 TYR cc_start: 0.8245 (t80) cc_final: 0.7995 (t80) REVERT: D 574 LYS cc_start: 0.8378 (mtpm) cc_final: 0.8073 (mtmm) REVERT: D 637 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7887 (p90) REVERT: D 646 ASN cc_start: 0.8221 (t0) cc_final: 0.7754 (t0) REVERT: D 670 ASP cc_start: 0.7567 (m-30) cc_final: 0.6770 (t0) REVERT: D 765 PRO cc_start: 0.8861 (Cg_exo) cc_final: 0.8459 (Cg_endo) REVERT: D 795 ASP cc_start: 0.8384 (p0) cc_final: 0.8167 (p0) REVERT: D 812 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7368 (mmtt) REVERT: D 919 MET cc_start: 0.7446 (mmt) cc_final: 0.6427 (mmm) REVERT: D 921 ASP cc_start: 0.8086 (p0) cc_final: 0.7772 (p0) REVERT: D 935 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7730 (mm110) REVERT: D 988 GLN cc_start: 0.8805 (tt0) cc_final: 0.8585 (tt0) REVERT: D 1097 VAL cc_start: 0.8611 (t) cc_final: 0.8275 (m) REVERT: D 1126 MET cc_start: 0.7990 (mtp) cc_final: 0.7058 (ttt) REVERT: D 1140 THR cc_start: 0.8700 (m) cc_final: 0.8145 (p) REVERT: D 1153 ASP cc_start: 0.6942 (t0) cc_final: 0.6705 (t0) REVERT: D 1255 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7264 (ttp80) REVERT: D 1318 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: E 137 ILE cc_start: 0.8879 (mm) cc_final: 0.8649 (tt) REVERT: E 367 GLU cc_start: 0.8439 (tp30) cc_final: 0.8153 (tp30) REVERT: E 457 GLN cc_start: 0.8291 (tt0) cc_final: 0.7474 (tp40) REVERT: E 709 MET cc_start: 0.8656 (mtp) cc_final: 0.8440 (ttm) REVERT: E 788 MET cc_start: 0.0591 (tpp) cc_final: 0.0331 (tpp) REVERT: E 795 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7312 (p0) REVERT: E 812 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8093 (mttt) REVERT: E 914 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7572 (mm-30) REVERT: E 1029 LEU cc_start: 0.8766 (tp) cc_final: 0.8490 (tp) REVERT: E 1055 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8367 (tp) REVERT: E 1076 ILE cc_start: 0.8949 (mm) cc_final: 0.8566 (mm) REVERT: E 1077 MET cc_start: 0.7798 (ttt) cc_final: 0.7548 (ttm) REVERT: E 1264 GLU cc_start: 0.8745 (mt-10) cc_final: 0.7839 (mp0) REVERT: E 1265 MET cc_start: 0.8638 (mtm) cc_final: 0.8281 (mtm) REVERT: E 1279 SER cc_start: 0.8365 (m) cc_final: 0.8037 (m) REVERT: E 1329 ASN cc_start: 0.8208 (p0) cc_final: 0.7906 (m110) REVERT: F 142 ASP cc_start: 0.7666 (t70) cc_final: 0.6143 (t70) REVERT: F 313 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8079 (t0) REVERT: F 333 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.6775 (tpt170) REVERT: F 366 MET cc_start: 0.8728 (mmm) cc_final: 0.8438 (mmm) REVERT: F 422 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8730 (tt) REVERT: F 441 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7742 (ttm110) REVERT: F 504 ASP cc_start: 0.8411 (t0) cc_final: 0.8137 (t0) REVERT: F 561 ASN cc_start: 0.8726 (t0) cc_final: 0.8482 (t0) REVERT: F 606 LEU cc_start: 0.9441 (mt) cc_final: 0.9023 (mt) REVERT: F 746 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: F 759 ASP cc_start: 0.8553 (t0) cc_final: 0.8188 (t0) REVERT: F 856 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8525 (mm) REVERT: F 928 ARG cc_start: 0.8389 (mtt90) cc_final: 0.8145 (mtm-85) REVERT: F 1031 TYR cc_start: 0.8802 (t80) cc_final: 0.8298 (t80) REVERT: F 1038 GLU cc_start: 0.6009 (tt0) cc_final: 0.5420 (tt0) REVERT: F 1265 MET cc_start: 0.8549 (mtt) cc_final: 0.8309 (mmm) REVERT: F 1279 SER cc_start: 0.8084 (m) cc_final: 0.7822 (m) REVERT: F 1318 GLU cc_start: 0.7363 (tt0) cc_final: 0.6787 (tt0) REVERT: G 198 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8656 (ptmt) REVERT: G 229 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7459 (tp40) REVERT: G 230 ASP cc_start: 0.8031 (t70) cc_final: 0.7501 (t70) REVERT: G 253 MET cc_start: 0.8155 (mmm) cc_final: 0.7800 (mmm) REVERT: G 259 MET cc_start: 0.7929 (ttt) cc_final: 0.7604 (ttt) REVERT: G 324 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7643 (mmtt) REVERT: G 339 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8853 (mt) REVERT: G 438 ASN cc_start: 0.8707 (t0) cc_final: 0.8204 (t0) REVERT: G 451 GLU cc_start: 0.7824 (tt0) cc_final: 0.7296 (tt0) REVERT: G 452 ASN cc_start: 0.7611 (m110) cc_final: 0.6482 (m110) REVERT: G 489 MET cc_start: 0.8172 (ttp) cc_final: 0.7867 (ttm) REVERT: G 524 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6332 (tm-30) REVERT: G 620 ILE cc_start: 0.9086 (mm) cc_final: 0.8826 (mt) REVERT: G 623 ASN cc_start: 0.8347 (t0) cc_final: 0.7881 (t0) REVERT: G 671 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8355 (p0) REVERT: G 682 GLN cc_start: 0.8540 (mt0) cc_final: 0.8226 (mt0) REVERT: G 709 MET cc_start: 0.8917 (ttm) cc_final: 0.8565 (mtp) REVERT: G 727 PHE cc_start: 0.9364 (t80) cc_final: 0.8897 (t80) REVERT: G 746 GLU cc_start: 0.7057 (tt0) cc_final: 0.6551 (tt0) REVERT: G 842 ASP cc_start: 0.7523 (t0) cc_final: 0.7101 (t0) REVERT: G 924 ASP cc_start: 0.7758 (t0) cc_final: 0.7558 (t0) REVERT: G 940 ARG cc_start: 0.7481 (ptm160) cc_final: 0.6972 (ptm-80) REVERT: G 942 HIS cc_start: 0.8517 (t-170) cc_final: 0.8317 (t-170) REVERT: G 988 GLN cc_start: 0.8214 (mm-40) cc_final: 0.8001 (tt0) REVERT: G 1003 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7174 (ptp90) REVERT: G 1038 GLU cc_start: 0.5566 (tt0) cc_final: 0.5217 (mp0) REVERT: G 1051 ARG cc_start: 0.8317 (ptp90) cc_final: 0.8000 (ptp90) REVERT: G 1061 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8794 (tp) REVERT: G 1118 THR cc_start: 0.8909 (t) cc_final: 0.8698 (t) REVERT: G 1144 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8343 (ttp-110) REVERT: G 1194 MET cc_start: 0.9031 (mmt) cc_final: 0.8729 (mmm) REVERT: G 1207 MET cc_start: 0.8070 (ppp) cc_final: 0.7633 (ppp) REVERT: G 1315 MET cc_start: 0.8466 (ppp) cc_final: 0.8113 (ppp) outliers start: 353 outliers final: 249 residues processed: 1797 average time/residue: 0.5516 time to fit residues: 1723.1217 Evaluate side-chains 1733 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1462 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 1019 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1140 THR Chi-restraints excluded: chain C residue 1179 THR Chi-restraints excluded: chain C residue 1189 ASP Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1314 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 995 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1085 ASP Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain D residue 1306 THR Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 491 ASN Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 698 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 795 ASP Chi-restraints excluded: chain E residue 814 THR Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 933 ASN Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1216 SER Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1293 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 746 GLU Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 795 ASP Chi-restraints excluded: chain F residue 832 MET Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 856 LEU Chi-restraints excluded: chain F residue 948 ILE Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1052 LEU Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1140 THR Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 559 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 838 GLU Chi-restraints excluded: chain G residue 849 MET Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 948 ILE Chi-restraints excluded: chain G residue 961 SER Chi-restraints excluded: chain G residue 970 LEU Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1050 LEU Chi-restraints excluded: chain G residue 1061 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1142 ASN Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1193 ILE Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1275 ASP Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 8.9990 chunk 669 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 436 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 744 optimal weight: 7.9990 chunk 617 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 390 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS B 346 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN C 693 ASN C 698 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1329 ASN ** D 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1234 GLN D1329 ASN E 148 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 ASN ** E1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN F 390 HIS ** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 802 GLN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 821 ASN G 933 ASN ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 62651 Z= 0.380 Angle : 0.718 17.411 85237 Z= 0.354 Chirality : 0.047 0.279 9752 Planarity : 0.005 0.076 11061 Dihedral : 6.835 169.519 8702 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 6.85 % Allowed : 20.35 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.09), residues: 7697 helix: -0.80 (0.10), residues: 2773 sheet: -1.89 (0.15), residues: 1007 loop : -1.30 (0.10), residues: 3917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 742 HIS 0.008 0.001 HIS D1121 PHE 0.030 0.002 PHE B 159 TYR 0.020 0.002 TYR F 922 ARG 0.011 0.001 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2003 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 461 poor density : 1542 time to evaluate : 5.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7929 (mmtp) REVERT: A 92 GLU cc_start: 0.8002 (mp0) cc_final: 0.6990 (tm-30) REVERT: A 116 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.4175 (p90) REVERT: A 226 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: A 235 LEU cc_start: 0.8000 (mm) cc_final: 0.7754 (mt) REVERT: A 263 ASN cc_start: 0.8774 (m110) cc_final: 0.8545 (m-40) REVERT: A 341 ASP cc_start: 0.8132 (p0) cc_final: 0.7747 (p0) REVERT: A 362 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 403 GLU cc_start: 0.7996 (tp30) cc_final: 0.6997 (tm-30) REVERT: A 434 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6773 (pt0) REVERT: A 475 LYS cc_start: 0.7224 (ptpp) cc_final: 0.6883 (mtpp) REVERT: A 484 ARG cc_start: 0.7750 (ttt180) cc_final: 0.7348 (ttt180) REVERT: A 485 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7128 (pmt-80) REVERT: A 502 MET cc_start: 0.8270 (tpt) cc_final: 0.7842 (tpp) REVERT: A 513 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 538 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8310 (mm-40) REVERT: A 539 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7492 (ttm110) REVERT: A 551 MET cc_start: 0.8042 (ttm) cc_final: 0.7508 (ttm) REVERT: A 587 MET cc_start: 0.8133 (mtp) cc_final: 0.7812 (mtm) REVERT: A 626 ILE cc_start: 0.8372 (pt) cc_final: 0.8129 (pt) REVERT: A 659 ASN cc_start: 0.8303 (t0) cc_final: 0.7821 (t0) REVERT: A 744 ARG cc_start: 0.8516 (ttm170) cc_final: 0.8229 (ptm160) REVERT: A 828 MET cc_start: 0.7607 (ppp) cc_final: 0.7132 (tmm) REVERT: A 830 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6996 (mp) REVERT: A 845 TYR cc_start: 0.7602 (t80) cc_final: 0.7387 (t80) REVERT: A 859 GLU cc_start: 0.7700 (pm20) cc_final: 0.7377 (pm20) REVERT: A 860 ASP cc_start: 0.8187 (p0) cc_final: 0.7373 (t0) REVERT: A 883 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 1000 ASP cc_start: 0.8241 (t0) cc_final: 0.7677 (m-30) REVERT: A 1103 ASP cc_start: 0.8185 (t0) cc_final: 0.7480 (t0) REVERT: A 1139 TYR cc_start: 0.8665 (t80) cc_final: 0.7757 (t80) REVERT: A 1144 SER cc_start: 0.8390 (m) cc_final: 0.7944 (t) REVERT: A 1157 SER cc_start: 0.9027 (m) cc_final: 0.8715 (p) REVERT: A 1174 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7678 (t) REVERT: A 1196 LYS cc_start: 0.8555 (mptt) cc_final: 0.8348 (mmtp) REVERT: B 146 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 193 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: B 204 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.7683 (ttp-110) REVERT: B 280 LEU cc_start: 0.7961 (pp) cc_final: 0.7654 (pp) REVERT: B 343 ASN cc_start: 0.8134 (t0) cc_final: 0.7629 (t0) REVERT: B 405 TYR cc_start: 0.7826 (t80) cc_final: 0.7587 (t80) REVERT: B 407 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 451 GLU cc_start: 0.8498 (tt0) cc_final: 0.8287 (tt0) REVERT: B 467 SER cc_start: 0.8927 (t) cc_final: 0.8467 (p) REVERT: C 135 LYS cc_start: 0.4727 (pptt) cc_final: 0.3856 (mttm) REVERT: C 174 PHE cc_start: 0.8133 (m-80) cc_final: 0.7282 (m-80) REVERT: C 223 LYS cc_start: 0.8832 (mttp) cc_final: 0.8536 (mmmm) REVERT: C 313 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8546 (t70) REVERT: C 361 ASN cc_start: 0.8740 (m-40) cc_final: 0.8343 (m-40) REVERT: C 377 LYS cc_start: 0.9259 (mttt) cc_final: 0.8664 (mtpt) REVERT: C 419 TYR cc_start: 0.8673 (m-80) cc_final: 0.8344 (m-80) REVERT: C 471 SER cc_start: 0.9030 (p) cc_final: 0.8671 (p) REVERT: C 544 TYR cc_start: 0.8452 (m-80) cc_final: 0.8225 (m-80) REVERT: C 576 ASP cc_start: 0.7969 (t0) cc_final: 0.7663 (t0) REVERT: C 629 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.5731 (ttp80) REVERT: C 661 ASN cc_start: 0.8315 (t0) cc_final: 0.8007 (t0) REVERT: C 698 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8081 (m-70) REVERT: C 723 ASN cc_start: 0.8131 (m110) cc_final: 0.7887 (m110) REVERT: C 847 ILE cc_start: 0.8422 (mt) cc_final: 0.8214 (tt) REVERT: C 861 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7136 (mm-30) REVERT: C 922 TYR cc_start: 0.7662 (m-10) cc_final: 0.7379 (m-10) REVERT: C 950 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7579 (t0) REVERT: C 1031 TYR cc_start: 0.8896 (t80) cc_final: 0.8513 (t80) REVERT: C 1038 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 1066 ARG cc_start: 0.8991 (mmt-90) cc_final: 0.8703 (tpp80) REVERT: C 1170 ASP cc_start: 0.8002 (t0) cc_final: 0.7796 (t70) REVERT: C 1225 GLU cc_start: 0.5341 (tp30) cc_final: 0.4043 (tt0) REVERT: C 1324 ASP cc_start: 0.8887 (t0) cc_final: 0.8636 (t70) REVERT: D 259 MET cc_start: 0.8244 (tpp) cc_final: 0.7815 (tpp) REVERT: D 300 LEU cc_start: 0.9058 (mt) cc_final: 0.8829 (mt) REVERT: D 333 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.6552 (tpt170) REVERT: D 497 LYS cc_start: 0.8662 (mmpt) cc_final: 0.8224 (mmtp) REVERT: D 500 GLU cc_start: 0.7420 (tp30) cc_final: 0.6963 (tp30) REVERT: D 526 ASN cc_start: 0.9102 (t0) cc_final: 0.8575 (t0) REVERT: D 552 ILE cc_start: 0.8905 (tp) cc_final: 0.8654 (tp) REVERT: D 574 LYS cc_start: 0.8925 (mtpm) cc_final: 0.8590 (mtmm) REVERT: D 637 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.7912 (p90) REVERT: D 646 ASN cc_start: 0.8382 (t0) cc_final: 0.8170 (t0) REVERT: D 698 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8331 (m-70) REVERT: D 728 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9005 (mmtp) REVERT: D 748 GLN cc_start: 0.7284 (pt0) cc_final: 0.6894 (pp30) REVERT: D 765 PRO cc_start: 0.8720 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: D 812 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7480 (mmtt) REVERT: D 909 TYR cc_start: 0.8962 (t80) cc_final: 0.8653 (t80) REVERT: D 914 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6985 (pt0) REVERT: D 921 ASP cc_start: 0.8239 (p0) cc_final: 0.7980 (p0) REVERT: D 935 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7782 (mm110) REVERT: D 968 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7722 (mtm110) REVERT: D 1044 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7969 (mtm-85) REVERT: D 1087 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8282 (p0) REVERT: D 1126 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.6994 (ttt) REVERT: D 1140 THR cc_start: 0.8800 (m) cc_final: 0.8239 (p) REVERT: D 1193 ILE cc_start: 0.8480 (tp) cc_final: 0.8210 (tt) REVERT: D 1227 MET cc_start: 0.8425 (mmt) cc_final: 0.8217 (mmt) REVERT: D 1255 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7472 (ttp-110) REVERT: D 1275 ASP cc_start: 0.6548 (m-30) cc_final: 0.6143 (p0) REVERT: D 1318 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: E 137 ILE cc_start: 0.8945 (mm) cc_final: 0.8686 (tt) REVERT: E 186 ASP cc_start: 0.8608 (m-30) cc_final: 0.8307 (m-30) REVERT: E 243 GLN cc_start: 0.8349 (mt0) cc_final: 0.7808 (mt0) REVERT: E 246 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7404 (mt-10) REVERT: E 333 ARG cc_start: 0.6472 (mmm-85) cc_final: 0.6048 (tpt170) REVERT: E 404 ASP cc_start: 0.8538 (t0) cc_final: 0.8207 (t70) REVERT: E 457 GLN cc_start: 0.8509 (tt0) cc_final: 0.7766 (tp40) REVERT: E 463 VAL cc_start: 0.9068 (m) cc_final: 0.8832 (p) REVERT: E 709 MET cc_start: 0.8783 (mtp) cc_final: 0.8502 (ttm) REVERT: E 728 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8668 (mtpp) REVERT: E 812 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8204 (mttt) REVERT: E 817 ASP cc_start: 0.7967 (m-30) cc_final: 0.7604 (m-30) REVERT: E 898 GLN cc_start: 0.8724 (tt0) cc_final: 0.8031 (tp40) REVERT: E 914 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7648 (mm-30) REVERT: E 1055 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8571 (tp) REVERT: E 1077 MET cc_start: 0.7841 (ttt) cc_final: 0.7572 (ttm) REVERT: E 1201 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8632 (tm) REVERT: E 1264 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7834 (mp0) REVERT: E 1265 MET cc_start: 0.8631 (mtm) cc_final: 0.8276 (mtm) REVERT: E 1329 ASN cc_start: 0.8316 (p0) cc_final: 0.8081 (m110) REVERT: F 313 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8180 (t70) REVERT: F 333 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.6718 (tpt170) REVERT: F 366 MET cc_start: 0.8692 (mmm) cc_final: 0.8409 (mmm) REVERT: F 413 MET cc_start: 0.8809 (mmm) cc_final: 0.8133 (mmm) REVERT: F 422 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8814 (tt) REVERT: F 441 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7787 (ttm110) REVERT: F 467 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8257 (mtpt) REVERT: F 504 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (t0) REVERT: F 561 ASN cc_start: 0.8770 (t0) cc_final: 0.8526 (t0) REVERT: F 606 LEU cc_start: 0.9416 (mt) cc_final: 0.9182 (mt) REVERT: F 637 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8413 (p90) REVERT: F 746 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7418 (tp30) REVERT: F 788 MET cc_start: 0.0305 (mmm) cc_final: -0.0054 (mmm) REVERT: F 808 GLN cc_start: 0.8303 (tt0) cc_final: 0.7891 (tt0) REVERT: F 822 MET cc_start: 0.9192 (tmm) cc_final: 0.8910 (tmm) REVERT: F 856 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8573 (mm) REVERT: F 861 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7842 (mm-30) REVERT: F 922 TYR cc_start: 0.6553 (m-10) cc_final: 0.5858 (m-10) REVERT: F 941 TYR cc_start: 0.8759 (p90) cc_final: 0.8400 (p90) REVERT: F 1038 GLU cc_start: 0.6267 (tt0) cc_final: 0.5935 (tt0) REVERT: F 1265 MET cc_start: 0.8730 (mtt) cc_final: 0.8462 (mtp) REVERT: F 1279 SER cc_start: 0.8349 (m) cc_final: 0.8112 (m) REVERT: F 1318 GLU cc_start: 0.7188 (tt0) cc_final: 0.6588 (tt0) REVERT: G 229 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7503 (tp40) REVERT: G 230 ASP cc_start: 0.8084 (t70) cc_final: 0.7603 (t70) REVERT: G 253 MET cc_start: 0.8410 (mmm) cc_final: 0.8120 (mmm) REVERT: G 259 MET cc_start: 0.7954 (ttt) cc_final: 0.7734 (ttt) REVERT: G 324 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7764 (mmtt) REVERT: G 339 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (mt) REVERT: G 438 ASN cc_start: 0.8807 (t0) cc_final: 0.8297 (t0) REVERT: G 451 GLU cc_start: 0.8243 (tt0) cc_final: 0.7638 (tt0) REVERT: G 452 ASN cc_start: 0.7829 (m110) cc_final: 0.7048 (m110) REVERT: G 524 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6408 (tm-30) REVERT: G 620 ILE cc_start: 0.9125 (mm) cc_final: 0.8812 (mt) REVERT: G 623 ASN cc_start: 0.8335 (t0) cc_final: 0.7857 (t0) REVERT: G 671 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8249 (p0) REVERT: G 682 GLN cc_start: 0.8615 (mt0) cc_final: 0.8243 (mt0) REVERT: G 709 MET cc_start: 0.9149 (ttm) cc_final: 0.8850 (mtp) REVERT: G 727 PHE cc_start: 0.9397 (t80) cc_final: 0.9052 (t80) REVERT: G 838 GLU cc_start: 0.7830 (mp0) cc_final: 0.7453 (pt0) REVERT: G 842 ASP cc_start: 0.7690 (t0) cc_final: 0.7303 (t0) REVERT: G 909 TYR cc_start: 0.7950 (t80) cc_final: 0.6531 (t80) REVERT: G 933 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7830 (t0) REVERT: G 939 ASN cc_start: 0.8242 (p0) cc_final: 0.7856 (m-40) REVERT: G 940 ARG cc_start: 0.7809 (ptm160) cc_final: 0.7232 (ptm-80) REVERT: G 1014 MET cc_start: 0.7824 (mmm) cc_final: 0.7572 (mmm) REVERT: G 1023 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7496 (ttm-80) REVERT: G 1038 GLU cc_start: 0.5723 (tt0) cc_final: 0.5134 (mp0) REVERT: G 1118 THR cc_start: 0.8998 (t) cc_final: 0.8788 (t) REVERT: G 1144 ARG cc_start: 0.8829 (ttp-110) cc_final: 0.8542 (ttp-110) REVERT: G 1194 MET cc_start: 0.9127 (mmt) cc_final: 0.8817 (mmm) REVERT: G 1207 MET cc_start: 0.8077 (ppp) cc_final: 0.7714 (tmm) outliers start: 461 outliers final: 332 residues processed: 1827 average time/residue: 0.5414 time to fit residues: 1710.4477 Evaluate side-chains 1785 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1421 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1068 SER Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1110 PHE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 698 HIS Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1019 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1140 THR Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1279 SER Chi-restraints excluded: chain C residue 1294 ASP Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1314 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 503 GLU Chi-restraints excluded: chain D residue 504 ASP Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 925 VAL Chi-restraints excluded: chain D residue 941 TYR Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 973 THR Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 995 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1044 ARG Chi-restraints excluded: chain D residue 1063 THR Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1085 ASP Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1126 MET Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain D residue 1306 THR Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1321 ASN Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 491 ASN Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain E residue 766 ILE Chi-restraints excluded: chain E residue 770 CYS Chi-restraints excluded: chain E residue 775 VAL Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 814 THR Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 865 ILE Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 933 ASN Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1035 ILE Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1223 SER Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1247 ASN Chi-restraints excluded: chain E residue 1293 VAL Chi-restraints excluded: chain E residue 1301 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 504 ASP Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 557 THR Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 760 THR Chi-restraints excluded: chain F residue 766 ILE Chi-restraints excluded: chain F residue 795 ASP Chi-restraints excluded: chain F residue 801 SER Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 832 MET Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 856 LEU Chi-restraints excluded: chain F residue 948 ILE Chi-restraints excluded: chain F residue 973 THR Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1052 LEU Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1140 THR Chi-restraints excluded: chain F residue 1155 ILE Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1269 THR Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain F residue 1313 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 243 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 400 GLU Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 487 SER Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 559 THR Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 713 MET Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 718 ASN Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 803 SER Chi-restraints excluded: chain G residue 821 ASN Chi-restraints excluded: chain G residue 823 ILE Chi-restraints excluded: chain G residue 849 MET Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 908 THR Chi-restraints excluded: chain G residue 933 ASN Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 948 ILE Chi-restraints excluded: chain G residue 961 SER Chi-restraints excluded: chain G residue 970 LEU Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1043 SER Chi-restraints excluded: chain G residue 1050 LEU Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1108 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1286 VAL Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 543 optimal weight: 0.1980 chunk 420 optimal weight: 0.4980 chunk 626 optimal weight: 4.9990 chunk 415 optimal weight: 4.9990 chunk 741 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 451 optimal weight: 0.7980 chunk 342 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS B 63 HIS B 346 ASN B 429 HIS B 466 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN B 527 GLN C 698 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 GLN ** D1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN E 382 HIS ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 933 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62651 Z= 0.171 Angle : 0.641 17.045 85237 Z= 0.312 Chirality : 0.044 0.226 9752 Planarity : 0.004 0.074 11061 Dihedral : 6.585 166.340 8700 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 4.75 % Allowed : 23.50 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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: -1.57 (0.10), residues: 7697 helix: -0.50 (0.10), residues: 2750 sheet: -1.83 (0.15), residues: 991 loop : -1.13 (0.10), residues: 3956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 309 HIS 0.025 0.001 HIS C 698 PHE 0.021 0.001 PHE G 568 TYR 0.030 0.001 TYR G 290 ARG 0.013 0.000 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1860 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1540 time to evaluate : 5.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7708 (mmtp) REVERT: A 116 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4358 (p90) REVERT: A 121 LYS cc_start: 0.7742 (mttp) cc_final: 0.7426 (ttmm) REVERT: A 122 MET cc_start: 0.7475 (tpp) cc_final: 0.7138 (tpp) REVERT: A 184 TYR cc_start: 0.7266 (p90) cc_final: 0.6944 (p90) REVERT: A 190 ASP cc_start: 0.7997 (t0) cc_final: 0.7750 (t0) REVERT: A 226 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: A 362 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: A 403 GLU cc_start: 0.7914 (tp30) cc_final: 0.7629 (tp30) REVERT: A 434 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: A 475 LYS cc_start: 0.7082 (ptpp) cc_final: 0.6801 (mttt) REVERT: A 485 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7235 (pmt-80) REVERT: A 502 MET cc_start: 0.8263 (tpt) cc_final: 0.7660 (tpp) REVERT: A 539 ARG cc_start: 0.7917 (ptp-170) cc_final: 0.7482 (ttm110) REVERT: A 587 MET cc_start: 0.8136 (mtp) cc_final: 0.7821 (mtm) REVERT: A 626 ILE cc_start: 0.8312 (pt) cc_final: 0.8080 (pt) REVERT: A 744 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8001 (ttm170) REVERT: A 758 MET cc_start: 0.8034 (tpp) cc_final: 0.7334 (tmm) REVERT: A 830 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7065 (mp) REVERT: A 845 TYR cc_start: 0.7544 (t80) cc_final: 0.7312 (t80) REVERT: A 860 ASP cc_start: 0.8121 (p0) cc_final: 0.7355 (t0) REVERT: A 883 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 884 MET cc_start: 0.8688 (ttp) cc_final: 0.8369 (ttt) REVERT: A 1000 ASP cc_start: 0.8265 (t0) cc_final: 0.7650 (m-30) REVERT: A 1103 ASP cc_start: 0.8218 (t0) cc_final: 0.7345 (t0) REVERT: A 1136 ASN cc_start: 0.7693 (m-40) cc_final: 0.6759 (m110) REVERT: A 1139 TYR cc_start: 0.8580 (t80) cc_final: 0.7728 (t80) REVERT: A 1144 SER cc_start: 0.8330 (m) cc_final: 0.7955 (t) REVERT: A 1157 SER cc_start: 0.8870 (m) cc_final: 0.8661 (p) REVERT: A 1174 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7590 (t) REVERT: A 1196 LYS cc_start: 0.8508 (mptt) cc_final: 0.8253 (mmtp) REVERT: B 47 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7570 (ttmm) REVERT: B 48 TYR cc_start: 0.7605 (m-10) cc_final: 0.7330 (m-10) REVERT: B 146 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7993 (mm-30) REVERT: B 193 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: B 240 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7507 (ptm160) REVERT: B 280 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7524 (pp) REVERT: B 288 LYS cc_start: 0.8428 (tttt) cc_final: 0.7726 (ttmm) REVERT: B 289 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 343 ASN cc_start: 0.8167 (t0) cc_final: 0.7730 (t0) REVERT: B 354 GLU cc_start: 0.8029 (mp0) cc_final: 0.7708 (mp0) REVERT: B 407 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 123 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 135 LYS cc_start: 0.4948 (pptt) cc_final: 0.3588 (ttpt) REVERT: C 174 PHE cc_start: 0.8258 (m-80) cc_final: 0.7468 (m-80) REVERT: C 223 LYS cc_start: 0.8793 (mttp) cc_final: 0.8581 (mmmm) REVERT: C 274 MET cc_start: 0.1360 (mmt) cc_final: 0.0917 (mmt) REVERT: C 361 ASN cc_start: 0.8798 (m-40) cc_final: 0.8441 (m-40) REVERT: C 377 LYS cc_start: 0.9226 (mttt) cc_final: 0.8649 (mtpt) REVERT: C 423 GLU cc_start: 0.7928 (tt0) cc_final: 0.7694 (tt0) REVERT: C 429 ILE cc_start: 0.8993 (mt) cc_final: 0.8758 (mp) REVERT: C 471 SER cc_start: 0.8961 (p) cc_final: 0.8603 (p) REVERT: C 576 ASP cc_start: 0.7967 (t0) cc_final: 0.7658 (t0) REVERT: C 629 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.5935 (ttp80) REVERT: C 638 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 734 ILE cc_start: 0.9013 (mm) cc_final: 0.8798 (mm) REVERT: C 861 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7163 (mm-30) REVERT: C 922 TYR cc_start: 0.7465 (m-10) cc_final: 0.7225 (m-10) REVERT: C 950 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7512 (t0) REVERT: C 1037 ILE cc_start: 0.9077 (mp) cc_final: 0.8861 (mp) REVERT: C 1038 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 1066 ARG cc_start: 0.8918 (mmt-90) cc_final: 0.8703 (tpp80) REVERT: C 1198 LYS cc_start: 0.9002 (tttp) cc_final: 0.8607 (tmtt) REVERT: C 1225 GLU cc_start: 0.5231 (tp30) cc_final: 0.4029 (tt0) REVERT: C 1308 ASN cc_start: 0.8976 (t0) cc_final: 0.8506 (t0) REVERT: C 1324 ASP cc_start: 0.8823 (t0) cc_final: 0.8461 (t70) REVERT: D 133 MET cc_start: 0.4919 (pmm) cc_final: 0.4009 (ptm) REVERT: D 147 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7710 (m) REVERT: D 259 MET cc_start: 0.8296 (tpp) cc_final: 0.7971 (tpp) REVERT: D 333 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.6734 (tpt170) REVERT: D 371 THR cc_start: 0.8342 (p) cc_final: 0.8054 (t) REVERT: D 500 GLU cc_start: 0.7245 (tp30) cc_final: 0.6804 (tp30) REVERT: D 526 ASN cc_start: 0.9005 (t0) cc_final: 0.8513 (t0) REVERT: D 552 ILE cc_start: 0.8861 (tp) cc_final: 0.8599 (tp) REVERT: D 574 LYS cc_start: 0.8867 (mtpm) cc_final: 0.8522 (mtmm) REVERT: D 637 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7993 (p90) REVERT: D 698 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8452 (m-70) REVERT: D 728 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8999 (mmtp) REVERT: D 812 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7463 (mmtt) REVERT: D 909 TYR cc_start: 0.8916 (t80) cc_final: 0.8604 (t80) REVERT: D 914 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6900 (pt0) REVERT: D 968 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7670 (mtm110) REVERT: D 1052 LEU cc_start: 0.8839 (mm) cc_final: 0.8541 (mp) REVERT: D 1087 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7939 (p0) REVERT: D 1097 VAL cc_start: 0.8667 (t) cc_final: 0.8427 (m) REVERT: D 1126 MET cc_start: 0.7827 (mtp) cc_final: 0.6976 (ttt) REVERT: D 1140 THR cc_start: 0.8981 (m) cc_final: 0.8396 (p) REVERT: D 1193 ILE cc_start: 0.8480 (tp) cc_final: 0.8184 (tt) REVERT: D 1255 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7416 (ttp80) REVERT: D 1318 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: E 137 ILE cc_start: 0.8958 (mm) cc_final: 0.8711 (tt) REVERT: E 186 ASP cc_start: 0.8567 (m-30) cc_final: 0.8242 (m-30) REVERT: E 243 GLN cc_start: 0.8325 (mt0) cc_final: 0.8038 (mt0) REVERT: E 404 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8196 (t70) REVERT: E 457 GLN cc_start: 0.8469 (tt0) cc_final: 0.7743 (tp40) REVERT: E 463 VAL cc_start: 0.9019 (m) cc_final: 0.8787 (p) REVERT: E 629 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.5414 (ttp-170) REVERT: E 653 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7787 (tpp80) REVERT: E 728 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8512 (mtpp) REVERT: E 788 MET cc_start: 0.1542 (tpp) cc_final: 0.0348 (tpt) REVERT: E 795 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7804 (p0) REVERT: E 812 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8123 (mttt) REVERT: E 817 ASP cc_start: 0.7879 (m-30) cc_final: 0.7554 (m-30) REVERT: E 898 GLN cc_start: 0.8651 (tt0) cc_final: 0.7964 (tp40) REVERT: E 914 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7530 (mm-30) REVERT: E 1055 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8428 (tp) REVERT: E 1076 ILE cc_start: 0.8970 (mm) cc_final: 0.8632 (mm) REVERT: E 1077 MET cc_start: 0.7887 (ttt) cc_final: 0.7613 (ttm) REVERT: E 1265 MET cc_start: 0.8555 (mtm) cc_final: 0.8228 (mtm) REVERT: F 313 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7927 (t0) REVERT: F 333 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.6835 (tpt170) REVERT: F 366 MET cc_start: 0.8611 (mmm) cc_final: 0.8328 (mmm) REVERT: F 411 CYS cc_start: 0.8943 (m) cc_final: 0.8379 (m) REVERT: F 422 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8826 (tt) REVERT: F 441 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7504 (ttm110) REVERT: F 467 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8224 (mtpt) REVERT: F 490 PHE cc_start: 0.8772 (m-10) cc_final: 0.8331 (m-10) REVERT: F 504 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8082 (t0) REVERT: F 561 ASN cc_start: 0.8728 (t0) cc_final: 0.8478 (t0) REVERT: F 746 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7371 (tp30) REVERT: F 808 GLN cc_start: 0.8288 (tt0) cc_final: 0.7905 (tt0) REVERT: F 822 MET cc_start: 0.9220 (tmm) cc_final: 0.8951 (tmm) REVERT: F 861 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7821 (mm-30) REVERT: F 922 TYR cc_start: 0.6092 (m-10) cc_final: 0.5706 (m-10) REVERT: F 1031 TYR cc_start: 0.8835 (t80) cc_final: 0.8042 (t80) REVERT: F 1033 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: F 1038 GLU cc_start: 0.6094 (tt0) cc_final: 0.5795 (tt0) REVERT: F 1083 ASP cc_start: 0.8530 (t0) cc_final: 0.8296 (t0) REVERT: F 1191 GLU cc_start: 0.6079 (tp30) cc_final: 0.5491 (tp30) REVERT: F 1265 MET cc_start: 0.8657 (mtt) cc_final: 0.8369 (mtp) REVERT: F 1279 SER cc_start: 0.8168 (m) cc_final: 0.7941 (m) REVERT: F 1295 HIS cc_start: 0.7862 (m90) cc_final: 0.7613 (m170) REVERT: F 1318 GLU cc_start: 0.7166 (tt0) cc_final: 0.6562 (tt0) REVERT: G 123 GLU cc_start: 0.8205 (pt0) cc_final: 0.7361 (pt0) REVERT: G 229 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7621 (tp40) REVERT: G 230 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7541 (t70) REVERT: G 324 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7668 (mmtt) REVERT: G 438 ASN cc_start: 0.8792 (t0) cc_final: 0.8282 (t0) REVERT: G 451 GLU cc_start: 0.8227 (tt0) cc_final: 0.7634 (tt0) REVERT: G 452 ASN cc_start: 0.7964 (m110) cc_final: 0.7129 (m110) REVERT: G 489 MET cc_start: 0.8132 (ttp) cc_final: 0.7888 (ttm) REVERT: G 524 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6411 (tm-30) REVERT: G 620 ILE cc_start: 0.9116 (mm) cc_final: 0.8791 (mt) REVERT: G 671 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8500 (p0) REVERT: G 682 GLN cc_start: 0.8599 (mt0) cc_final: 0.8217 (mt0) REVERT: G 709 MET cc_start: 0.8928 (ttm) cc_final: 0.8582 (mtp) REVERT: G 727 PHE cc_start: 0.9365 (t80) cc_final: 0.8967 (t80) REVERT: G 746 GLU cc_start: 0.6528 (tt0) cc_final: 0.6031 (tt0) REVERT: G 842 ASP cc_start: 0.8016 (t0) cc_final: 0.7785 (t0) REVERT: G 909 TYR cc_start: 0.7993 (t80) cc_final: 0.6720 (t80) REVERT: G 939 ASN cc_start: 0.8189 (p0) cc_final: 0.7862 (m-40) REVERT: G 940 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7336 (ptm-80) REVERT: G 965 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8197 (mmm160) REVERT: G 1003 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7188 (ptm160) REVERT: G 1014 MET cc_start: 0.7894 (mmm) cc_final: 0.7677 (mmm) REVERT: G 1038 GLU cc_start: 0.5600 (tt0) cc_final: 0.4967 (mp0) REVERT: G 1077 MET cc_start: 0.8050 (mtp) cc_final: 0.7712 (mtp) REVERT: G 1118 THR cc_start: 0.8876 (t) cc_final: 0.8637 (t) REVERT: G 1144 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8485 (ttp-110) REVERT: G 1207 MET cc_start: 0.8144 (ppp) cc_final: 0.7843 (ppp) REVERT: G 1315 MET cc_start: 0.8431 (ppp) cc_final: 0.8177 (ppp) outliers start: 320 outliers final: 224 residues processed: 1724 average time/residue: 0.5570 time to fit residues: 1669.0200 Evaluate side-chains 1712 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1458 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1110 PHE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 491 ASN Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 736 SER Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1279 SER Chi-restraints excluded: chain C residue 1314 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 995 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1321 ASN Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 698 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 795 ASP Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 933 ASN Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1293 VAL Chi-restraints excluded: chain E residue 1301 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 504 ASP Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 795 ASP Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 832 MET Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 948 ILE Chi-restraints excluded: chain F residue 1027 THR Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1226 ASP Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain F residue 1308 ASN Chi-restraints excluded: chain F residue 1314 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 400 GLU Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 703 SER Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 758 ILE Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 908 THR Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 948 ILE Chi-restraints excluded: chain G residue 970 LEU Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1142 ASN Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1193 ILE Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1275 ASP Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 145 optimal weight: 0.0060 chunk 143 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 504 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 582 optimal weight: 9.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN A 898 HIS ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 346 ASN B 414 ASN B 429 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1329 ASN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 777 GLN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 62651 Z= 0.254 Angle : 0.663 17.293 85237 Z= 0.323 Chirality : 0.045 0.299 9752 Planarity : 0.004 0.076 11061 Dihedral : 6.551 166.413 8700 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 4.72 % Allowed : 24.16 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.07 % 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: -1.48 (0.10), residues: 7697 helix: -0.41 (0.10), residues: 2767 sheet: -1.75 (0.16), residues: 996 loop : -1.12 (0.10), residues: 3934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 309 HIS 0.009 0.001 HIS B 63 PHE 0.023 0.001 PHE B 159 TYR 0.025 0.001 TYR G 290 ARG 0.013 0.001 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1799 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1481 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7688 (mmtp) REVERT: A 116 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.4467 (p90) REVERT: A 121 LYS cc_start: 0.7754 (mttp) cc_final: 0.7327 (ttmm) REVERT: A 122 MET cc_start: 0.7496 (tpp) cc_final: 0.7199 (tpp) REVERT: A 190 ASP cc_start: 0.7909 (t0) cc_final: 0.7673 (t0) REVERT: A 226 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: A 362 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 403 GLU cc_start: 0.7918 (tp30) cc_final: 0.7617 (tp30) REVERT: A 434 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: A 475 LYS cc_start: 0.7110 (ptpp) cc_final: 0.6887 (mttt) REVERT: A 485 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7138 (pmt-80) REVERT: A 502 MET cc_start: 0.8297 (tpt) cc_final: 0.7713 (tpp) REVERT: A 539 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7368 (ttm110) REVERT: A 587 MET cc_start: 0.8108 (mtp) cc_final: 0.7830 (mtm) REVERT: A 591 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 659 ASN cc_start: 0.8238 (t0) cc_final: 0.7918 (t0) REVERT: A 744 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8076 (ptm160) REVERT: A 758 MET cc_start: 0.7937 (tpp) cc_final: 0.7410 (tmm) REVERT: A 807 ASN cc_start: 0.8226 (m-40) cc_final: 0.7796 (m110) REVERT: A 830 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7122 (mp) REVERT: A 845 TYR cc_start: 0.7583 (t80) cc_final: 0.7375 (t80) REVERT: A 860 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7405 (t0) REVERT: A 883 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: A 1000 ASP cc_start: 0.8509 (t0) cc_final: 0.7928 (m-30) REVERT: A 1103 ASP cc_start: 0.8231 (t0) cc_final: 0.7191 (t0) REVERT: A 1136 ASN cc_start: 0.7497 (m-40) cc_final: 0.6754 (m110) REVERT: A 1139 TYR cc_start: 0.8605 (t80) cc_final: 0.7843 (t80) REVERT: A 1157 SER cc_start: 0.9058 (m) cc_final: 0.8723 (p) REVERT: A 1174 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7562 (t) REVERT: B 47 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7732 (ttmm) REVERT: B 146 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 193 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: B 240 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7344 (ptm160) REVERT: B 254 GLU cc_start: 0.8305 (pm20) cc_final: 0.7858 (pm20) REVERT: B 280 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7570 (pp) REVERT: B 288 LYS cc_start: 0.8409 (tttt) cc_final: 0.7727 (ttmm) REVERT: B 289 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 321 MET cc_start: 0.8597 (ttp) cc_final: 0.7683 (ttp) REVERT: B 343 ASN cc_start: 0.8224 (t0) cc_final: 0.7783 (t0) REVERT: B 354 GLU cc_start: 0.8080 (mp0) cc_final: 0.7819 (mp0) REVERT: B 407 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8116 (mm) REVERT: C 135 LYS cc_start: 0.4937 (pptt) cc_final: 0.3543 (ttpp) REVERT: C 174 PHE cc_start: 0.8285 (m-80) cc_final: 0.7427 (m-80) REVERT: C 223 LYS cc_start: 0.8808 (mttp) cc_final: 0.8606 (mmmm) REVERT: C 274 MET cc_start: 0.1692 (mmt) cc_final: 0.1030 (mmt) REVERT: C 313 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8471 (t70) REVERT: C 361 ASN cc_start: 0.8801 (m-40) cc_final: 0.8425 (m-40) REVERT: C 377 LYS cc_start: 0.9223 (mttt) cc_final: 0.8638 (mtpt) REVERT: C 423 GLU cc_start: 0.7956 (tt0) cc_final: 0.7688 (tt0) REVERT: C 471 SER cc_start: 0.8982 (p) cc_final: 0.8628 (p) REVERT: C 576 ASP cc_start: 0.8007 (t0) cc_final: 0.7692 (t0) REVERT: C 629 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.5695 (ttp80) REVERT: C 638 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8265 (t) REVERT: C 713 MET cc_start: 0.8131 (ttm) cc_final: 0.7909 (ttm) REVERT: C 861 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7298 (mm-30) REVERT: C 922 TYR cc_start: 0.7517 (m-10) cc_final: 0.7253 (m-10) REVERT: C 1038 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7703 (pt0) REVERT: C 1066 ARG cc_start: 0.8944 (mmt-90) cc_final: 0.8709 (tpp80) REVERT: C 1198 LYS cc_start: 0.9003 (tttp) cc_final: 0.8590 (tmtt) REVERT: C 1225 GLU cc_start: 0.5337 (tp30) cc_final: 0.4037 (tt0) REVERT: C 1308 ASN cc_start: 0.9066 (t0) cc_final: 0.8500 (t0) REVERT: D 133 MET cc_start: 0.4793 (pmm) cc_final: 0.4033 (ptm) REVERT: D 147 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7738 (m) REVERT: D 259 MET cc_start: 0.8320 (tpp) cc_final: 0.8099 (tpp) REVERT: D 333 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.6702 (tpt170) REVERT: D 371 THR cc_start: 0.8422 (p) cc_final: 0.8116 (t) REVERT: D 497 LYS cc_start: 0.8708 (mmpt) cc_final: 0.8173 (mttt) REVERT: D 500 GLU cc_start: 0.7518 (tp30) cc_final: 0.7305 (mm-30) REVERT: D 526 ASN cc_start: 0.9023 (t0) cc_final: 0.8498 (t0) REVERT: D 552 ILE cc_start: 0.8880 (tp) cc_final: 0.8629 (tp) REVERT: D 574 LYS cc_start: 0.8963 (mtpm) cc_final: 0.8612 (mtmm) REVERT: D 588 LEU cc_start: 0.9378 (tp) cc_final: 0.9109 (tp) REVERT: D 604 MET cc_start: 0.8725 (mmt) cc_final: 0.8084 (mmt) REVERT: D 637 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8102 (p90) REVERT: D 698 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8512 (m-70) REVERT: D 728 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9021 (mmtp) REVERT: D 812 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7446 (mmtt) REVERT: D 909 TYR cc_start: 0.8933 (t80) cc_final: 0.8606 (t80) REVERT: D 914 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6933 (pt0) REVERT: D 1087 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8254 (p0) REVERT: D 1126 MET cc_start: 0.7833 (mtp) cc_final: 0.7049 (ttt) REVERT: D 1140 THR cc_start: 0.9010 (m) cc_final: 0.8450 (p) REVERT: D 1193 ILE cc_start: 0.8560 (tp) cc_final: 0.8287 (tt) REVERT: D 1255 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7399 (tmm-80) REVERT: D 1318 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: E 137 ILE cc_start: 0.8993 (mm) cc_final: 0.8743 (tt) REVERT: E 186 ASP cc_start: 0.8624 (m-30) cc_final: 0.8301 (m-30) REVERT: E 333 ARG cc_start: 0.6490 (mmm-85) cc_final: 0.6280 (mmt180) REVERT: E 404 ASP cc_start: 0.8525 (t0) cc_final: 0.8218 (t70) REVERT: E 457 GLN cc_start: 0.8526 (tt0) cc_final: 0.7788 (tp40) REVERT: E 463 VAL cc_start: 0.9062 (m) cc_final: 0.8855 (p) REVERT: E 629 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.5653 (ttp-110) REVERT: E 653 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7511 (tpp-160) REVERT: E 788 MET cc_start: 0.1657 (tpp) cc_final: 0.0513 (tpt) REVERT: E 795 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7861 (p0) REVERT: E 812 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8158 (mttt) REVERT: E 817 ASP cc_start: 0.7892 (m-30) cc_final: 0.7589 (m-30) REVERT: E 898 GLN cc_start: 0.8699 (tt0) cc_final: 0.8034 (tp40) REVERT: E 914 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7562 (mm-30) REVERT: E 1029 LEU cc_start: 0.8855 (tp) cc_final: 0.8623 (tp) REVERT: E 1055 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8474 (tp) REVERT: E 1077 MET cc_start: 0.7922 (ttt) cc_final: 0.7606 (ttm) REVERT: E 1227 MET cc_start: 0.8252 (mmt) cc_final: 0.7485 (ptt) REVERT: E 1231 TYR cc_start: 0.8882 (m-80) cc_final: 0.8478 (m-80) REVERT: E 1265 MET cc_start: 0.8561 (mtm) cc_final: 0.8231 (mtm) REVERT: E 1269 THR cc_start: 0.8925 (p) cc_final: 0.8710 (p) REVERT: F 289 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8342 (t) REVERT: F 301 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8342 (mp) REVERT: F 313 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.7865 (t0) REVERT: F 333 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.6913 (tpt170) REVERT: F 366 MET cc_start: 0.8662 (mmm) cc_final: 0.8377 (mmm) REVERT: F 411 CYS cc_start: 0.8921 (m) cc_final: 0.8366 (m) REVERT: F 413 MET cc_start: 0.8774 (mmm) cc_final: 0.8160 (mmm) REVERT: F 422 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8814 (tt) REVERT: F 441 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7522 (ttm110) REVERT: F 467 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8207 (mtpt) REVERT: F 490 PHE cc_start: 0.8753 (m-10) cc_final: 0.8369 (m-10) REVERT: F 504 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (t0) REVERT: F 561 ASN cc_start: 0.8739 (t0) cc_final: 0.8489 (t0) REVERT: F 746 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7381 (tp30) REVERT: F 788 MET cc_start: 0.0424 (mmm) cc_final: 0.0168 (mmm) REVERT: F 808 GLN cc_start: 0.8340 (tt0) cc_final: 0.7953 (tt0) REVERT: F 822 MET cc_start: 0.9129 (tmm) cc_final: 0.8874 (tmm) REVERT: F 861 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7884 (mm-30) REVERT: F 922 TYR cc_start: 0.6318 (m-10) cc_final: 0.5822 (m-10) REVERT: F 1191 GLU cc_start: 0.5728 (tp30) cc_final: 0.4925 (tp30) REVERT: F 1265 MET cc_start: 0.8748 (mtt) cc_final: 0.8270 (mtm) REVERT: F 1279 SER cc_start: 0.8215 (m) cc_final: 0.7971 (m) REVERT: F 1318 GLU cc_start: 0.7169 (tt0) cc_final: 0.6556 (tt0) REVERT: G 123 GLU cc_start: 0.8214 (pt0) cc_final: 0.7385 (pt0) REVERT: G 229 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7571 (tp40) REVERT: G 230 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7558 (t70) REVERT: G 243 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8378 (mm-40) REVERT: G 290 TYR cc_start: 0.7972 (p90) cc_final: 0.7696 (p90) REVERT: G 324 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7636 (mmtt) REVERT: G 367 GLU cc_start: 0.5398 (tm-30) cc_final: 0.5071 (tm-30) REVERT: G 438 ASN cc_start: 0.8870 (t0) cc_final: 0.8335 (t0) REVERT: G 451 GLU cc_start: 0.8152 (tt0) cc_final: 0.7625 (tt0) REVERT: G 452 ASN cc_start: 0.8023 (m110) cc_final: 0.7238 (m110) REVERT: G 524 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6439 (tm-30) REVERT: G 577 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8687 (tp-100) REVERT: G 620 ILE cc_start: 0.9106 (mm) cc_final: 0.8788 (mt) REVERT: G 639 ASN cc_start: 0.7819 (p0) cc_final: 0.7579 (p0) REVERT: G 671 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8377 (p0) REVERT: G 682 GLN cc_start: 0.8506 (mt0) cc_final: 0.7989 (mt0) REVERT: G 727 PHE cc_start: 0.9385 (t80) cc_final: 0.9026 (t80) REVERT: G 746 GLU cc_start: 0.6525 (tt0) cc_final: 0.6049 (tt0) REVERT: G 842 ASP cc_start: 0.7981 (t0) cc_final: 0.7725 (t0) REVERT: G 909 TYR cc_start: 0.8057 (t80) cc_final: 0.6734 (t80) REVERT: G 939 ASN cc_start: 0.8220 (p0) cc_final: 0.7948 (m-40) REVERT: G 940 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7409 (ptm-80) REVERT: G 1003 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7203 (ptm160) REVERT: G 1033 ASP cc_start: 0.8340 (t0) cc_final: 0.8016 (t0) REVERT: G 1038 GLU cc_start: 0.5664 (tt0) cc_final: 0.4980 (mp0) REVERT: G 1077 MET cc_start: 0.8020 (mtp) cc_final: 0.7693 (mtp) REVERT: G 1118 THR cc_start: 0.8924 (t) cc_final: 0.8701 (t) REVERT: G 1207 MET cc_start: 0.8121 (ppp) cc_final: 0.7826 (ppp) REVERT: G 1315 MET cc_start: 0.8377 (ppp) cc_final: 0.8103 (ppp) outliers start: 318 outliers final: 244 residues processed: 1662 average time/residue: 0.5525 time to fit residues: 1589.9444 Evaluate side-chains 1690 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1415 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1110 PHE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 491 ASN Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 736 SER Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1189 ASP Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain C residue 1279 SER Chi-restraints excluded: chain C residue 1314 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 973 THR Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 995 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1321 ASN Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 795 ASP Chi-restraints excluded: chain E residue 820 ILE Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 933 ASN Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1293 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 504 ASP Chi-restraints excluded: chain F residue 512 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 760 THR Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 973 THR Chi-restraints excluded: chain F residue 1027 THR Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1226 ASP Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain F residue 1308 ASN Chi-restraints excluded: chain F residue 1313 ASP Chi-restraints excluded: chain F residue 1314 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 559 THR Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 703 SER Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 758 ILE Chi-restraints excluded: chain G residue 820 ILE Chi-restraints excluded: chain G residue 823 ILE Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 908 THR Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 970 LEU Chi-restraints excluded: chain G residue 976 THR Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1103 HIS Chi-restraints excluded: chain G residue 1108 SER Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1142 ASN Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1193 ILE Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 0.8980 chunk 710 optimal weight: 10.0000 chunk 647 optimal weight: 0.0870 chunk 690 optimal weight: 6.9990 chunk 709 optimal weight: 7.9990 chunk 415 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 542 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 624 optimal weight: 0.2980 chunk 653 optimal weight: 9.9990 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS B 63 HIS B 346 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 62651 Z= 0.164 Angle : 0.635 17.076 85237 Z= 0.307 Chirality : 0.043 0.270 9752 Planarity : 0.004 0.074 11061 Dihedral : 6.421 166.097 8700 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.26 % Allowed : 24.83 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.05 % 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: -1.31 (0.10), residues: 7697 helix: -0.21 (0.10), residues: 2733 sheet: -1.67 (0.16), residues: 965 loop : -1.06 (0.10), residues: 3999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 309 HIS 0.011 0.001 HIS B 63 PHE 0.022 0.001 PHE F 607 TYR 0.024 0.001 TYR G 558 ARG 0.014 0.000 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1827 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1540 time to evaluate : 5.224 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 24 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7801 (mmtp) REVERT: A 116 TYR cc_start: 0.5411 (OUTLIER) cc_final: 0.4607 (p90) REVERT: A 121 LYS cc_start: 0.7642 (mttp) cc_final: 0.7276 (ttmm) REVERT: A 122 MET cc_start: 0.7470 (tpp) cc_final: 0.7125 (tpp) REVERT: A 184 TYR cc_start: 0.7154 (p90) cc_final: 0.6946 (p90) REVERT: A 190 ASP cc_start: 0.8059 (t0) cc_final: 0.7743 (t0) REVERT: A 362 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 403 GLU cc_start: 0.7967 (tp30) cc_final: 0.7634 (tp30) REVERT: A 434 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: A 485 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7330 (pmt-80) REVERT: A 502 MET cc_start: 0.8261 (tpt) cc_final: 0.7692 (tpp) REVERT: A 511 TYR cc_start: 0.7866 (m-10) cc_final: 0.7622 (m-10) REVERT: A 539 ARG cc_start: 0.7844 (ptp-170) cc_final: 0.7419 (ttm110) REVERT: A 551 MET cc_start: 0.7879 (ttm) cc_final: 0.7467 (ttm) REVERT: A 587 MET cc_start: 0.8027 (mtp) cc_final: 0.7783 (mtm) REVERT: A 591 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 626 ILE cc_start: 0.8462 (pt) cc_final: 0.8248 (pt) REVERT: A 845 TYR cc_start: 0.7547 (t80) cc_final: 0.7282 (t80) REVERT: A 860 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7393 (t0) REVERT: A 883 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 1000 ASP cc_start: 0.8490 (t0) cc_final: 0.7910 (m-30) REVERT: A 1103 ASP cc_start: 0.8178 (t0) cc_final: 0.7207 (t0) REVERT: A 1136 ASN cc_start: 0.7656 (m-40) cc_final: 0.6817 (m110) REVERT: A 1139 TYR cc_start: 0.8579 (t80) cc_final: 0.7859 (t80) REVERT: A 1157 SER cc_start: 0.8910 (m) cc_final: 0.8645 (p) REVERT: A 1174 CYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7603 (t) REVERT: B 47 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7720 (ttmm) REVERT: B 146 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 204 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7557 (ttp-110) REVERT: B 240 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7338 (ptm160) REVERT: B 247 GLU cc_start: 0.8291 (tt0) cc_final: 0.7893 (tt0) REVERT: B 254 GLU cc_start: 0.8234 (pm20) cc_final: 0.7896 (pm20) REVERT: B 277 ASP cc_start: 0.8276 (m-30) cc_final: 0.7911 (m-30) REVERT: B 288 LYS cc_start: 0.8426 (tttt) cc_final: 0.7729 (ttmm) REVERT: B 289 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7312 (mm-30) REVERT: B 321 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7477 (tpp) REVERT: B 343 ASN cc_start: 0.8231 (t0) cc_final: 0.7814 (t0) REVERT: B 354 GLU cc_start: 0.8052 (mp0) cc_final: 0.7795 (mp0) REVERT: B 407 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8011 (mm) REVERT: C 135 LYS cc_start: 0.4533 (pptt) cc_final: 0.3374 (ttpt) REVERT: C 174 PHE cc_start: 0.8276 (m-80) cc_final: 0.7503 (m-80) REVERT: C 253 MET cc_start: 0.8539 (tpp) cc_final: 0.8071 (tpp) REVERT: C 274 MET cc_start: 0.1886 (mmt) cc_final: 0.1318 (mmt) REVERT: C 313 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8450 (t0) REVERT: C 374 ASP cc_start: 0.8116 (m-30) cc_final: 0.7869 (m-30) REVERT: C 377 LYS cc_start: 0.9220 (mttt) cc_final: 0.8747 (mtpt) REVERT: C 429 ILE cc_start: 0.8966 (mt) cc_final: 0.8735 (mp) REVERT: C 456 ASN cc_start: 0.8591 (t0) cc_final: 0.8072 (t0) REVERT: C 471 SER cc_start: 0.8948 (p) cc_final: 0.8605 (p) REVERT: C 576 ASP cc_start: 0.7946 (t0) cc_final: 0.7639 (t0) REVERT: C 629 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.5504 (ttp80) REVERT: C 638 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8242 (t) REVERT: C 734 ILE cc_start: 0.9011 (mm) cc_final: 0.8800 (mm) REVERT: C 861 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 1038 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7545 (pt0) REVERT: C 1104 ARG cc_start: 0.8362 (ttt90) cc_final: 0.7910 (ptm-80) REVERT: C 1198 LYS cc_start: 0.9060 (tttp) cc_final: 0.8511 (tmtt) REVERT: C 1225 GLU cc_start: 0.5267 (tp30) cc_final: 0.4033 (tt0) REVERT: C 1308 ASN cc_start: 0.8997 (t0) cc_final: 0.8483 (t0) REVERT: D 147 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7719 (m) REVERT: D 259 MET cc_start: 0.8290 (tpp) cc_final: 0.8059 (tpp) REVERT: D 333 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.6707 (tpt170) REVERT: D 371 THR cc_start: 0.8354 (p) cc_final: 0.8119 (t) REVERT: D 497 LYS cc_start: 0.8615 (mmpt) cc_final: 0.8309 (mmtp) REVERT: D 526 ASN cc_start: 0.8984 (t0) cc_final: 0.8496 (t0) REVERT: D 552 ILE cc_start: 0.8794 (tp) cc_final: 0.8501 (tp) REVERT: D 574 LYS cc_start: 0.8896 (mtpm) cc_final: 0.8553 (mtmm) REVERT: D 637 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8013 (p90) REVERT: D 698 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8552 (m-70) REVERT: D 728 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9012 (mmtp) REVERT: D 812 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7429 (mmtt) REVERT: D 909 TYR cc_start: 0.8879 (t80) cc_final: 0.8569 (t80) REVERT: D 914 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6966 (pt0) REVERT: D 1030 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8183 (ttm110) REVERT: D 1126 MET cc_start: 0.7789 (mtp) cc_final: 0.7324 (ttt) REVERT: D 1139 MET cc_start: 0.7707 (tpp) cc_final: 0.7062 (tpp) REVERT: D 1140 THR cc_start: 0.8981 (m) cc_final: 0.8378 (p) REVERT: D 1193 ILE cc_start: 0.8554 (tp) cc_final: 0.8302 (tt) REVERT: D 1207 MET cc_start: 0.7814 (ttm) cc_final: 0.7385 (ttt) REVERT: D 1255 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7424 (ttp80) REVERT: D 1265 MET cc_start: 0.8551 (mtm) cc_final: 0.8309 (mmm) REVERT: D 1318 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: E 137 ILE cc_start: 0.9000 (mm) cc_final: 0.8763 (tt) REVERT: E 186 ASP cc_start: 0.8606 (m-30) cc_final: 0.8284 (m-30) REVERT: E 333 ARG cc_start: 0.6384 (mmm-85) cc_final: 0.6077 (tpt170) REVERT: E 404 ASP cc_start: 0.8451 (t0) cc_final: 0.8168 (t70) REVERT: E 457 GLN cc_start: 0.8481 (tt0) cc_final: 0.7764 (tp40) REVERT: E 463 VAL cc_start: 0.9035 (m) cc_final: 0.8824 (p) REVERT: E 629 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.5509 (ttp-170) REVERT: E 698 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7282 (t-90) REVERT: E 788 MET cc_start: 0.1559 (tpp) cc_final: 0.0409 (tpt) REVERT: E 795 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7810 (p0) REVERT: E 812 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8103 (mttt) REVERT: E 817 ASP cc_start: 0.7792 (m-30) cc_final: 0.7498 (m-30) REVERT: E 898 GLN cc_start: 0.8635 (tt0) cc_final: 0.7984 (tp40) REVERT: E 914 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7502 (mm-30) REVERT: E 1055 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8545 (tp) REVERT: E 1076 ILE cc_start: 0.8901 (mm) cc_final: 0.8534 (mm) REVERT: E 1077 MET cc_start: 0.7944 (ttt) cc_final: 0.7677 (ttm) REVERT: E 1265 MET cc_start: 0.8542 (mtm) cc_final: 0.8229 (mtm) REVERT: E 1269 THR cc_start: 0.8743 (p) cc_final: 0.8525 (p) REVERT: F 313 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.7927 (t0) REVERT: F 317 MET cc_start: 0.8099 (mmt) cc_final: 0.7354 (mtt) REVERT: F 333 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6808 (tpt170) REVERT: F 366 MET cc_start: 0.8580 (mmm) cc_final: 0.8295 (mmm) REVERT: F 411 CYS cc_start: 0.8940 (m) cc_final: 0.8371 (m) REVERT: F 422 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8782 (tt) REVERT: F 441 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7479 (ttm110) REVERT: F 467 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8164 (mtpt) REVERT: F 490 PHE cc_start: 0.8696 (m-10) cc_final: 0.8442 (m-10) REVERT: F 547 GLU cc_start: 0.8519 (mp0) cc_final: 0.8075 (mp0) REVERT: F 561 ASN cc_start: 0.8736 (t0) cc_final: 0.8477 (t0) REVERT: F 583 GLU cc_start: 0.8636 (pm20) cc_final: 0.8406 (pm20) REVERT: F 746 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7366 (tp30) REVERT: F 808 GLN cc_start: 0.8256 (tt0) cc_final: 0.8035 (tt0) REVERT: F 822 MET cc_start: 0.9059 (tmm) cc_final: 0.8789 (tmm) REVERT: F 861 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7850 (mm-30) REVERT: F 870 ASP cc_start: 0.9255 (t0) cc_final: 0.8986 (t0) REVERT: F 922 TYR cc_start: 0.5942 (m-10) cc_final: 0.5456 (m-10) REVERT: F 961 SER cc_start: 0.9081 (m) cc_final: 0.8648 (p) REVERT: F 1191 GLU cc_start: 0.5879 (tp30) cc_final: 0.5189 (tp30) REVERT: F 1279 SER cc_start: 0.8139 (m) cc_final: 0.7896 (m) REVERT: F 1315 MET cc_start: 0.8595 (ttp) cc_final: 0.8371 (ttp) REVERT: F 1318 GLU cc_start: 0.7141 (tt0) cc_final: 0.6530 (tt0) REVERT: G 123 GLU cc_start: 0.8188 (pt0) cc_final: 0.7346 (pt0) REVERT: G 229 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7745 (tp40) REVERT: G 230 ASP cc_start: 0.7993 (t70) cc_final: 0.7453 (t70) REVERT: G 324 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7571 (mmtt) REVERT: G 438 ASN cc_start: 0.8848 (t0) cc_final: 0.8320 (t0) REVERT: G 451 GLU cc_start: 0.8141 (tt0) cc_final: 0.7633 (tt0) REVERT: G 452 ASN cc_start: 0.8045 (m110) cc_final: 0.7249 (m110) REVERT: G 489 MET cc_start: 0.8145 (ttp) cc_final: 0.7926 (ttm) REVERT: G 524 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6357 (tm-30) REVERT: G 577 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8691 (tp-100) REVERT: G 606 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8655 (mm) REVERT: G 620 ILE cc_start: 0.9094 (mm) cc_final: 0.8782 (mt) REVERT: G 639 ASN cc_start: 0.7626 (p0) cc_final: 0.7380 (p0) REVERT: G 671 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8399 (p0) REVERT: G 682 GLN cc_start: 0.8480 (mt0) cc_final: 0.7991 (mt0) REVERT: G 709 MET cc_start: 0.8983 (ttm) cc_final: 0.8608 (mtp) REVERT: G 727 PHE cc_start: 0.9399 (t80) cc_final: 0.9088 (t80) REVERT: G 746 GLU cc_start: 0.6622 (tt0) cc_final: 0.6134 (tt0) REVERT: G 909 TYR cc_start: 0.8008 (t80) cc_final: 0.6775 (t80) REVERT: G 939 ASN cc_start: 0.8114 (p0) cc_final: 0.7853 (m110) REVERT: G 940 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7423 (ptm-80) REVERT: G 965 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8179 (mmm160) REVERT: G 1003 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7301 (ptm160) REVERT: G 1033 ASP cc_start: 0.8301 (t0) cc_final: 0.7975 (t0) REVERT: G 1038 GLU cc_start: 0.5632 (tt0) cc_final: 0.4992 (mp0) REVERT: G 1077 MET cc_start: 0.8074 (mtp) cc_final: 0.7792 (mtp) REVERT: G 1207 MET cc_start: 0.8167 (ppp) cc_final: 0.7790 (tmm) REVERT: G 1315 MET cc_start: 0.8328 (ppp) cc_final: 0.8056 (ppp) outliers start: 287 outliers final: 232 residues processed: 1693 average time/residue: 0.5408 time to fit residues: 1587.3261 Evaluate side-chains 1725 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1468 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1110 PHE Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 SER Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1007 THR Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1189 ASP Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 719 ASN Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 973 THR Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1104 ARG Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1321 ASN Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 698 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 795 ASP Chi-restraints excluded: chain E residue 820 ILE Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1055 LEU Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1091 ASP Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1301 VAL Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 760 THR Chi-restraints excluded: chain F residue 795 ASP Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 832 MET Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 973 THR Chi-restraints excluded: chain F residue 1027 THR Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1226 ASP Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain F residue 1313 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 400 GLU Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 534 ASN Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 577 GLN Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 703 SER Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 758 ILE Chi-restraints excluded: chain G residue 803 SER Chi-restraints excluded: chain G residue 820 ILE Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 908 THR Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 970 LEU Chi-restraints excluded: chain G residue 976 THR Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1193 ILE Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 2.9990 chunk 453 optimal weight: 0.6980 chunk 730 optimal weight: 9.9990 chunk 445 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 507 optimal weight: 20.0000 chunk 766 optimal weight: 5.9990 chunk 705 optimal weight: 4.9990 chunk 610 optimal weight: 0.0470 chunk 63 optimal weight: 6.9990 chunk 471 optimal weight: 0.5980 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 311 ASN ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN G 640 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62651 Z= 0.163 Angle : 0.645 17.148 85237 Z= 0.310 Chirality : 0.044 0.308 9752 Planarity : 0.004 0.074 11061 Dihedral : 6.350 166.492 8700 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 4.05 % Allowed : 25.22 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.05 % 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: -1.22 (0.10), residues: 7697 helix: -0.11 (0.10), residues: 2732 sheet: -1.64 (0.16), residues: 977 loop : -1.02 (0.10), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 309 HIS 0.006 0.001 HIS A 364 PHE 0.017 0.001 PHE G 568 TYR 0.023 0.001 TYR G 558 ARG 0.014 0.000 ARG E1051 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1785 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1512 time to evaluate : 5.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7784 (mmtp) REVERT: A 116 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.4697 (p90) REVERT: A 121 LYS cc_start: 0.7592 (mttp) cc_final: 0.7168 (ttmm) REVERT: A 122 MET cc_start: 0.7463 (tpp) cc_final: 0.7139 (tpp) REVERT: A 190 ASP cc_start: 0.7884 (t0) cc_final: 0.7564 (t0) REVERT: A 362 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: A 412 HIS cc_start: 0.7243 (t70) cc_final: 0.7032 (t-170) REVERT: A 434 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6412 (pt0) REVERT: A 485 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7323 (pmt-80) REVERT: A 502 MET cc_start: 0.8271 (tpt) cc_final: 0.7690 (tpp) REVERT: A 511 TYR cc_start: 0.7852 (m-10) cc_final: 0.7632 (m-10) REVERT: A 532 MET cc_start: 0.7869 (mtt) cc_final: 0.7393 (mtt) REVERT: A 539 ARG cc_start: 0.7917 (ptp-170) cc_final: 0.7474 (ttm110) REVERT: A 551 MET cc_start: 0.7844 (ttm) cc_final: 0.7432 (ttm) REVERT: A 587 MET cc_start: 0.7957 (mtp) cc_final: 0.7704 (mtm) REVERT: A 591 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 626 ILE cc_start: 0.8343 (pt) cc_final: 0.8116 (pt) REVERT: A 758 MET cc_start: 0.7803 (mmt) cc_final: 0.7148 (mtt) REVERT: A 830 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7069 (mp) REVERT: A 845 TYR cc_start: 0.7600 (t80) cc_final: 0.7343 (t80) REVERT: A 860 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7443 (t0) REVERT: A 883 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 1000 ASP cc_start: 0.8395 (t0) cc_final: 0.7745 (m-30) REVERT: A 1103 ASP cc_start: 0.8191 (t0) cc_final: 0.7250 (t0) REVERT: A 1136 ASN cc_start: 0.7663 (m-40) cc_final: 0.6706 (m110) REVERT: A 1157 SER cc_start: 0.8750 (m) cc_final: 0.8548 (p) REVERT: A 1174 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7578 (t) REVERT: B 47 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7650 (ttmm) REVERT: B 146 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 204 ARG cc_start: 0.8337 (ttp-110) cc_final: 0.7514 (ttp-110) REVERT: B 240 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7342 (ptm160) REVERT: B 247 GLU cc_start: 0.8167 (tt0) cc_final: 0.7779 (tt0) REVERT: B 277 ASP cc_start: 0.8240 (m-30) cc_final: 0.7885 (m-30) REVERT: B 288 LYS cc_start: 0.8460 (tttt) cc_final: 0.7734 (ttmm) REVERT: B 289 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 321 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 343 ASN cc_start: 0.8261 (t0) cc_final: 0.7949 (t0) REVERT: B 354 GLU cc_start: 0.8044 (mp0) cc_final: 0.7788 (mp0) REVERT: B 407 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7997 (mm) REVERT: C 135 LYS cc_start: 0.4490 (pptt) cc_final: 0.3364 (ttpt) REVERT: C 174 PHE cc_start: 0.8262 (m-80) cc_final: 0.7481 (m-80) REVERT: C 253 MET cc_start: 0.8481 (tpp) cc_final: 0.7919 (tpp) REVERT: C 274 MET cc_start: 0.1950 (mmt) cc_final: 0.1354 (mmt) REVERT: C 313 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8265 (t0) REVERT: C 374 ASP cc_start: 0.8132 (m-30) cc_final: 0.7898 (m-30) REVERT: C 377 LYS cc_start: 0.9222 (mttt) cc_final: 0.8751 (mtpt) REVERT: C 429 ILE cc_start: 0.8953 (mt) cc_final: 0.8726 (mp) REVERT: C 456 ASN cc_start: 0.8537 (t0) cc_final: 0.8039 (t0) REVERT: C 471 SER cc_start: 0.8944 (p) cc_final: 0.8615 (p) REVERT: C 576 ASP cc_start: 0.8137 (t0) cc_final: 0.7775 (t0) REVERT: C 629 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.5523 (ttp80) REVERT: C 638 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (t) REVERT: C 734 ILE cc_start: 0.9017 (mm) cc_final: 0.8814 (mm) REVERT: C 861 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7237 (mm-30) REVERT: C 872 ILE cc_start: 0.9144 (pt) cc_final: 0.8913 (tp) REVERT: C 1038 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7542 (pt0) REVERT: C 1198 LYS cc_start: 0.9038 (tttp) cc_final: 0.8506 (tmtt) REVERT: C 1225 GLU cc_start: 0.5243 (tp30) cc_final: 0.4001 (tt0) REVERT: C 1308 ASN cc_start: 0.8879 (t0) cc_final: 0.8445 (t0) REVERT: D 133 MET cc_start: 0.5379 (pmm) cc_final: 0.4470 (ppp) REVERT: D 147 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7747 (m) REVERT: D 259 MET cc_start: 0.8279 (tpp) cc_final: 0.8068 (tpp) REVERT: D 274 MET cc_start: 0.6818 (ttm) cc_final: 0.6498 (mtp) REVERT: D 333 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.6675 (tpt170) REVERT: D 497 LYS cc_start: 0.8605 (mmpt) cc_final: 0.8070 (mtmt) REVERT: D 526 ASN cc_start: 0.8984 (t0) cc_final: 0.8512 (t0) REVERT: D 552 ILE cc_start: 0.8780 (tp) cc_final: 0.8486 (tp) REVERT: D 574 LYS cc_start: 0.8865 (mtpm) cc_final: 0.8489 (mtmm) REVERT: D 604 MET cc_start: 0.8481 (mmt) cc_final: 0.7976 (mmt) REVERT: D 637 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8034 (p90) REVERT: D 698 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8607 (m-70) REVERT: D 728 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9007 (mmtp) REVERT: D 804 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8475 (mm) REVERT: D 812 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7379 (mmtt) REVERT: D 898 GLN cc_start: 0.8610 (tt0) cc_final: 0.8099 (tp40) REVERT: D 909 TYR cc_start: 0.8886 (t80) cc_final: 0.8543 (t80) REVERT: D 914 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6968 (pt0) REVERT: D 1126 MET cc_start: 0.7774 (mtp) cc_final: 0.7400 (ttt) REVERT: D 1139 MET cc_start: 0.7696 (tpp) cc_final: 0.7053 (tpp) REVERT: D 1140 THR cc_start: 0.9010 (m) cc_final: 0.8454 (p) REVERT: D 1193 ILE cc_start: 0.8550 (tp) cc_final: 0.8304 (tt) REVERT: D 1255 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7438 (ttp80) REVERT: D 1265 MET cc_start: 0.8458 (mtm) cc_final: 0.8165 (mmm) REVERT: D 1318 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: E 137 ILE cc_start: 0.9004 (mm) cc_final: 0.8775 (tt) REVERT: E 186 ASP cc_start: 0.8597 (m-30) cc_final: 0.8269 (m-30) REVERT: E 207 ASP cc_start: 0.7271 (p0) cc_final: 0.6919 (p0) REVERT: E 333 ARG cc_start: 0.6392 (mmm-85) cc_final: 0.6070 (tpt170) REVERT: E 361 ASN cc_start: 0.9118 (m-40) cc_final: 0.8821 (m110) REVERT: E 404 ASP cc_start: 0.8441 (t0) cc_final: 0.8168 (t70) REVERT: E 457 GLN cc_start: 0.8404 (tt0) cc_final: 0.7627 (tp40) REVERT: E 463 VAL cc_start: 0.9034 (m) cc_final: 0.8823 (p) REVERT: E 629 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.5588 (ttp-170) REVERT: E 698 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7301 (t-90) REVERT: E 788 MET cc_start: 0.1568 (tpp) cc_final: 0.0435 (tpt) REVERT: E 795 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7829 (p0) REVERT: E 812 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8102 (mttt) REVERT: E 817 ASP cc_start: 0.7774 (m-30) cc_final: 0.7491 (m-30) REVERT: E 898 GLN cc_start: 0.8619 (tt0) cc_final: 0.7989 (tp40) REVERT: E 914 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7497 (mm-30) REVERT: E 950 ASP cc_start: 0.7777 (m-30) cc_final: 0.7318 (m-30) REVERT: E 1076 ILE cc_start: 0.8871 (mm) cc_final: 0.8504 (mm) REVERT: E 1077 MET cc_start: 0.8028 (ttt) cc_final: 0.7768 (ttm) REVERT: E 1227 MET cc_start: 0.8185 (mmt) cc_final: 0.7459 (ptt) REVERT: E 1265 MET cc_start: 0.8532 (mtm) cc_final: 0.8224 (mtm) REVERT: E 1269 THR cc_start: 0.8677 (p) cc_final: 0.8460 (p) REVERT: F 313 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7920 (t0) REVERT: F 317 MET cc_start: 0.8061 (mmt) cc_final: 0.7498 (mtt) REVERT: F 333 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.6985 (tpt170) REVERT: F 366 MET cc_start: 0.8496 (mmm) cc_final: 0.8201 (mmm) REVERT: F 411 CYS cc_start: 0.8936 (m) cc_final: 0.8371 (m) REVERT: F 422 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8750 (tt) REVERT: F 441 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7475 (ttm110) REVERT: F 467 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8146 (mtpt) REVERT: F 489 MET cc_start: 0.7364 (tpp) cc_final: 0.6988 (mmt) REVERT: F 547 GLU cc_start: 0.8524 (mp0) cc_final: 0.8098 (mp0) REVERT: F 561 ASN cc_start: 0.8730 (t0) cc_final: 0.8470 (t0) REVERT: F 630 ASN cc_start: 0.8518 (p0) cc_final: 0.8307 (p0) REVERT: F 746 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7357 (tp30) REVERT: F 808 GLN cc_start: 0.8249 (tt0) cc_final: 0.8038 (tt0) REVERT: F 822 MET cc_start: 0.8949 (tmm) cc_final: 0.8734 (tmm) REVERT: F 861 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7888 (mm-30) REVERT: F 870 ASP cc_start: 0.9225 (t0) cc_final: 0.8972 (t0) REVERT: F 922 TYR cc_start: 0.6227 (m-10) cc_final: 0.5530 (m-10) REVERT: F 961 SER cc_start: 0.9078 (m) cc_final: 0.8646 (p) REVERT: F 1031 TYR cc_start: 0.8848 (t80) cc_final: 0.8645 (t80) REVERT: F 1191 GLU cc_start: 0.6041 (tp30) cc_final: 0.5317 (tp30) REVERT: F 1265 MET cc_start: 0.8661 (mtt) cc_final: 0.8408 (mtp) REVERT: F 1279 SER cc_start: 0.8147 (m) cc_final: 0.7893 (m) REVERT: F 1315 MET cc_start: 0.8619 (ttp) cc_final: 0.8370 (ttp) REVERT: F 1318 GLU cc_start: 0.7149 (tt0) cc_final: 0.6525 (tt0) REVERT: G 123 GLU cc_start: 0.8176 (pt0) cc_final: 0.7497 (pt0) REVERT: G 229 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7729 (tp40) REVERT: G 230 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7332 (t70) REVERT: G 324 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7584 (mmtt) REVERT: G 438 ASN cc_start: 0.8842 (t0) cc_final: 0.8316 (t0) REVERT: G 451 GLU cc_start: 0.8153 (tt0) cc_final: 0.7646 (tt0) REVERT: G 452 ASN cc_start: 0.8046 (m110) cc_final: 0.7257 (m110) REVERT: G 489 MET cc_start: 0.8158 (ttp) cc_final: 0.7938 (ttm) REVERT: G 524 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6363 (tm-30) REVERT: G 620 ILE cc_start: 0.9091 (mm) cc_final: 0.8778 (mt) REVERT: G 639 ASN cc_start: 0.7505 (p0) cc_final: 0.7249 (p0) REVERT: G 671 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8540 (p0) REVERT: G 682 GLN cc_start: 0.8471 (mt0) cc_final: 0.8008 (mt0) REVERT: G 709 MET cc_start: 0.8985 (ttm) cc_final: 0.8624 (mtp) REVERT: G 727 PHE cc_start: 0.9420 (t80) cc_final: 0.9124 (t80) REVERT: G 746 GLU cc_start: 0.6642 (tt0) cc_final: 0.6158 (tt0) REVERT: G 909 TYR cc_start: 0.8067 (t80) cc_final: 0.6877 (t80) REVERT: G 939 ASN cc_start: 0.8056 (p0) cc_final: 0.7800 (m110) REVERT: G 940 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7448 (ptm-80) REVERT: G 965 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8140 (mmm160) REVERT: G 1003 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7281 (ptm160) REVERT: G 1014 MET cc_start: 0.7966 (mmm) cc_final: 0.7698 (mmm) REVERT: G 1029 LEU cc_start: 0.8389 (mp) cc_final: 0.8137 (mp) REVERT: G 1033 ASP cc_start: 0.8286 (t0) cc_final: 0.7982 (t0) REVERT: G 1038 GLU cc_start: 0.5635 (tt0) cc_final: 0.4993 (mp0) REVERT: G 1077 MET cc_start: 0.8193 (mtp) cc_final: 0.7992 (mtp) REVERT: G 1207 MET cc_start: 0.8200 (ppp) cc_final: 0.7800 (ppp) REVERT: G 1265 MET cc_start: 0.8551 (mtp) cc_final: 0.8119 (mtp) REVERT: G 1315 MET cc_start: 0.8385 (ppp) cc_final: 0.8107 (ppp) outliers start: 273 outliers final: 218 residues processed: 1659 average time/residue: 0.5530 time to fit residues: 1597.8584 Evaluate side-chains 1701 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1458 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1149 PHE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 637 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 SER Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 870 ASP Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 971 MET Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain C residue 1007 THR Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1033 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1189 ASP Chi-restraints excluded: chain C residue 1275 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 472 GLU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 637 TYR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 698 HIS Chi-restraints excluded: chain D residue 728 LYS Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1028 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1074 VAL Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1104 ARG Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1189 ASP Chi-restraints excluded: chain D residue 1191 GLU Chi-restraints excluded: chain D residue 1318 GLU Chi-restraints excluded: chain D residue 1321 ASN Chi-restraints excluded: chain D residue 1332 ASN Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 582 SER Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 637 TYR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 698 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain E residue 792 VAL Chi-restraints excluded: chain E residue 795 ASP Chi-restraints excluded: chain E residue 820 ILE Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 890 THR Chi-restraints excluded: chain E residue 901 VAL Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1037 ILE Chi-restraints excluded: chain E residue 1043 SER Chi-restraints excluded: chain E residue 1089 VAL Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain E residue 1238 VAL Chi-restraints excluded: chain E residue 1301 VAL Chi-restraints excluded: chain E residue 1311 THR Chi-restraints excluded: chain E residue 1320 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 637 TYR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain F residue 698 HIS Chi-restraints excluded: chain F residue 736 SER Chi-restraints excluded: chain F residue 752 VAL Chi-restraints excluded: chain F residue 760 THR Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 832 MET Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 851 THR Chi-restraints excluded: chain F residue 948 ILE Chi-restraints excluded: chain F residue 973 THR Chi-restraints excluded: chain F residue 1027 THR Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1037 ILE Chi-restraints excluded: chain F residue 1062 ILE Chi-restraints excluded: chain F residue 1074 VAL Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1091 ASP Chi-restraints excluded: chain F residue 1092 VAL Chi-restraints excluded: chain F residue 1188 VAL Chi-restraints excluded: chain F residue 1216 SER Chi-restraints excluded: chain F residue 1226 ASP Chi-restraints excluded: chain F residue 1286 VAL Chi-restraints excluded: chain F residue 1313 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 400 GLU Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 637 TYR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 640 GLN Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 668 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 703 SER Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 758 ILE Chi-restraints excluded: chain G residue 803 SER Chi-restraints excluded: chain G residue 890 THR Chi-restraints excluded: chain G residue 908 THR Chi-restraints excluded: chain G residue 945 VAL Chi-restraints excluded: chain G residue 976 THR Chi-restraints excluded: chain G residue 995 THR Chi-restraints excluded: chain G residue 1003 ARG Chi-restraints excluded: chain G residue 1028 VAL Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1092 VAL Chi-restraints excluded: chain G residue 1110 LEU Chi-restraints excluded: chain G residue 1189 ASP Chi-restraints excluded: chain G residue 1193 ILE Chi-restraints excluded: chain G residue 1267 THR Chi-restraints excluded: chain G residue 1301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 649 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 562 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 611 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 627 optimal weight: 0.0270 chunk 77 optimal weight: 5.9990 overall best weight: 6.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS B 346 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN C 572 ASN ** D 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** D 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** E 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN G 821 ASN ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103726 restraints weight = 104304.570| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.33 r_work: 0.3117 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.8222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 62651 Z= 0.332 Angle : 0.709 17.439 85237 Z= 0.345 Chirality : 0.047 0.379 9752 Planarity : 0.005 0.078 11061 Dihedral : 6.518 167.263 8700 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 4.47 % Allowed : 24.88 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.07 % 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: -1.33 (0.10), residues: 7697 helix: -0.22 (0.10), residues: 2768 sheet: -1.80 (0.15), residues: 1000 loop : -1.04 (0.10), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.007 0.001 HIS A1036 PHE 0.033 0.002 PHE D 449 TYR 0.031 0.002 TYR A 184 ARG 0.014 0.001 ARG F 188 =============================================================================== Job complete usr+sys time: 23822.11 seconds wall clock time: 413 minutes 33.07 seconds (24813.07 seconds total)