Starting phenix.real_space_refine on Tue Apr 16 16:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/04_2024/6rqt_4985.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 Zn 6 6.06 5 P 32 5.49 5 S 192 5.16 5 C 25171 2.51 5 N 6861 2.21 5 O 7558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 146": "NH1" <-> "NH2" Residue "M TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39820 Number of models: 1 Model: "" Number of chains: 22 Chain: "T" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 364 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "U" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 11571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1466, 11571 Classifications: {'peptide': 1466} Link IDs: {'PTRANS': 59, 'TRANS': 1406} Chain breaks: 7 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 59, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3100 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 2 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain breaks: 3 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1438 SG CYS A 102 66.174 111.496 29.449 1.00134.25 S ATOM 1463 SG CYS A 105 68.758 109.770 27.061 1.00125.68 S ATOM 2266 SG CYS A 233 70.503 112.479 28.832 1.00138.82 S ATOM 2288 SG CYS A 236 67.323 113.009 25.923 1.00128.29 S ATOM 1118 SG CYS A 62 63.193 63.201 50.586 1.00126.53 S ATOM 20809 SG CYS B1104 77.104 70.352 40.906 1.00103.26 S ATOM 20835 SG CYS B1107 75.752 73.677 41.530 1.00 96.18 S ATOM 20982 SG CYS B1128 73.462 69.899 41.474 1.00123.10 S ATOM 21010 SG CYS B1131 75.928 72.325 38.130 1.00111.40 S ATOM 29889 SG CYS I 33 31.910 146.308 76.107 1.00151.43 S ATOM 30212 SG CYS J 10 79.847 70.030 122.752 1.00 86.08 S ATOM 30498 SG CYS J 46 78.102 69.462 125.806 1.00 91.81 S ATOM 31544 SG CYS L 34 35.059 66.052 108.191 1.00149.28 S ATOM 31648 SG CYS L 48 34.232 65.092 103.963 1.00155.75 S Time building chain proxies: 19.68, per 1000 atoms: 0.49 Number of scatterers: 39820 At special positions: 0 Unit cell: (156.562, 177.791, 164.523, 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) Zn 6 29.99 S 192 16.00 P 32 15.00 O 7558 8.00 N 6861 7.00 C 25171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.33 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 12 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 51 sheets defined 28.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.523A pdb=" N ILE A 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 4.355A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.658A pdb=" N LEU A 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.650A pdb=" N CYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.790A pdb=" N ASN A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 130 through 134 removed outlier: 4.113A pdb=" N TYR A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.993A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.603A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.946A pdb=" N GLY A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A 269 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.969A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 328' Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.926A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 339' Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.875A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.543A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.677A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.518A pdb=" N MET A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.595A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 4.039A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.646A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.902A pdb=" N TYR A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 625' Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.639A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.710A pdb=" N GLN A 656 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.523A pdb=" N THR A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.953A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.565A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 793 through 801 removed outlier: 4.223A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 809 removed outlier: 4.460A pdb=" N VAL A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.500A pdb=" N PHE A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.905A pdb=" N ILE A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 removed outlier: 3.505A pdb=" N SER A 850 " --> pdb=" O LEU A 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 847 through 850' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.988A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 908 removed outlier: 4.234A pdb=" N THR A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 993 through 999 removed outlier: 3.545A pdb=" N CYS A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1008 removed outlier: 3.739A pdb=" N GLU A1004 " --> pdb=" O MET A1000 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.558A pdb=" N THR A1024 " --> pdb=" O GLN A1020 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.543A pdb=" N LYS A1059 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.868A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1092 through 1109 removed outlier: 3.902A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.579A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 removed outlier: 3.745A pdb=" N SER A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.927A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 4.298A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1256 removed outlier: 4.012A pdb=" N ASP A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 3.699A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1333 " --> pdb=" O ILE A1329 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 removed outlier: 3.598A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 3.573A pdb=" N GLU A1490 " --> pdb=" O VAL A1486 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1549 removed outlier: 3.580A pdb=" N ALA A1548 " --> pdb=" O ASP A1545 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A1549 " --> pdb=" O VAL A1546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1545 through 1549' Processing helix chain 'A' and resid 1554 through 1558 Processing helix chain 'A' and resid 1565 through 1573 removed outlier: 4.121A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1589 removed outlier: 3.548A pdb=" N ILE A1585 " --> pdb=" O HIS A1581 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A1589 " --> pdb=" O ILE A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 4.006A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.565A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.737A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.708A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.760A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.655A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 285 through 290 removed outlier: 4.203A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.514A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.545A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.787A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 removed outlier: 3.518A pdb=" N VAL B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.743A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 386 removed outlier: 4.407A pdb=" N PHE B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N MET B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.948A pdb=" N GLN B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.759A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 removed outlier: 4.181A pdb=" N GLN B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 457 through 467 removed outlier: 4.339A pdb=" N TYR B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.689A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 512 " --> pdb=" O PHE B 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 508 through 512' Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.673A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 removed outlier: 4.068A pdb=" N ARG B 634 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.534A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.788A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 714 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.566A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 759 removed outlier: 4.013A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 835 through 839 removed outlier: 4.119A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 839' Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.787A pdb=" N SER B 966 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 968 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 969 " --> pdb=" O GLU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.592A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 removed outlier: 3.718A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1090 Processing helix chain 'B' and resid 1136 through 1138 No H-bonds generated for 'chain 'B' and resid 1136 through 1138' Processing helix chain 'B' and resid 1179 through 1193 removed outlier: 4.404A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B1190 " --> pdb=" O ASP B1186 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B1193 " --> pdb=" O LEU B1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.771A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.135A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.807A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.668A pdb=" N GLU C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.623A pdb=" N ASP D 95 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 96 " --> pdb=" O GLN D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.696A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.988A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.694A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.988A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.554A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.812A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.115A pdb=" N LYS G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 19' Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.501A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.527A pdb=" N HIS G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 66 " --> pdb=" O MET G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 67 through 70 removed outlier: 3.659A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 70' Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'J' and resid 15 through 23 removed outlier: 3.954A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.677A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.529A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.785A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.792A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 removed outlier: 3.510A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.891A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 159 through 164 removed outlier: 3.544A pdb=" N ASP M 163 " --> pdb=" O ILE M 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER M 164 " --> pdb=" O ASP M 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 159 through 164' Processing helix chain 'M' and resid 209 through 214 removed outlier: 3.549A pdb=" N GLN M 214 " --> pdb=" O LYS M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 250 removed outlier: 4.127A pdb=" N LYS M 246 " --> pdb=" O VAL M 243 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP M 248 " --> pdb=" O LYS M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 266 removed outlier: 3.552A pdb=" N TYR M 264 " --> pdb=" O GLN M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 285 removed outlier: 3.823A pdb=" N GLU M 285 " --> pdb=" O THR M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 295 Processing helix chain 'M' and resid 308 through 313 removed outlier: 3.511A pdb=" N ARG M 312 " --> pdb=" O GLY M 308 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER M 313 " --> pdb=" O GLN M 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 308 through 313' Processing helix chain 'M' and resid 337 through 341 removed outlier: 3.764A pdb=" N ASP M 340 " --> pdb=" O MET M 337 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN M 341 " --> pdb=" O HIS M 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 337 through 341' Processing helix chain 'M' and resid 346 through 351 Processing helix chain 'M' and resid 363 through 367 removed outlier: 3.764A pdb=" N VAL M 366 " --> pdb=" O LEU M 363 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU M 367 " --> pdb=" O PHE M 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 363 through 367' Processing helix chain 'M' and resid 377 through 381 removed outlier: 4.399A pdb=" N GLU M 380 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA M 381 " --> pdb=" O GLN M 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 377 through 381' Processing helix chain 'O' and resid 49 through 54 removed outlier: 3.659A pdb=" N ARG O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 100 removed outlier: 3.520A pdb=" N LEU O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.250A pdb=" N ILE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.751A pdb=" N TYR O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE O 137 " --> pdb=" O LEU O 133 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 161 removed outlier: 3.530A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 173 through 180 removed outlier: 3.757A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE O 179 " --> pdb=" O MET O 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 212 removed outlier: 4.001A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL O 209 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR O 212 " --> pdb=" O LEU O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 204 through 212' Processing helix chain 'O' and resid 214 through 222 removed outlier: 4.186A pdb=" N LEU O 218 " --> pdb=" O ASN O 214 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 234 removed outlier: 4.444A pdb=" N LEU O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 246 removed outlier: 4.018A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 343 removed outlier: 4.062A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR O 337 " --> pdb=" O ASP O 333 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR O 341 " --> pdb=" O THR O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 352 removed outlier: 3.759A pdb=" N LEU O 352 " --> pdb=" O PRO O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 362 removed outlier: 3.858A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN O 362 " --> pdb=" O VAL O 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 357 through 362' Processing helix chain 'O' and resid 365 through 370 Processing helix chain 'O' and resid 393 through 401 removed outlier: 3.624A pdb=" N ASP O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 423 removed outlier: 4.319A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER O 420 " --> pdb=" O LYS O 416 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 443 removed outlier: 4.002A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 456 removed outlier: 3.871A pdb=" N VAL O 454 " --> pdb=" O LEU O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 475 through 481 Processing helix chain 'O' and resid 501 through 506 removed outlier: 4.066A pdb=" N PHE O 506 " --> pdb=" O LEU O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 527 removed outlier: 3.564A pdb=" N LEU O 526 " --> pdb=" O ASN O 523 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 535 Processing helix chain 'O' and resid 543 through 551 removed outlier: 3.970A pdb=" N ASN O 548 " --> pdb=" O ILE O 544 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN O 549 " --> pdb=" O GLU O 545 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU O 550 " --> pdb=" O ASN O 546 " (cutoff:3.500A) Processing helix chain 'O' and resid 602 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.675A pdb=" N PHE A 252 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.745A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 481 removed outlier: 3.753A pdb=" N ALA A 479 " --> pdb=" O ARG B1047 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG B1047 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 481 " --> pdb=" O GLN B1045 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 487 removed outlier: 5.746A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.503A pdb=" N VAL A 497 " --> pdb=" O ARG A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA9, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.915A pdb=" N MET A 589 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 601 " --> pdb=" O MET A 589 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 750 through 751 removed outlier: 3.680A pdb=" N SER A 751 " --> pdb=" O VAL A 769 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 3.558A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1267 through 1272 removed outlier: 3.683A pdb=" N ILE A1271 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU A1471 " --> pdb=" O TYR A1460 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR A1460 " --> pdb=" O GLU A1471 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A1473 " --> pdb=" O THR A1458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 104 removed outlier: 3.894A pdb=" N SER B 144 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 196 removed outlier: 4.158A pdb=" N ILE B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 202 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 486 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB9, first strand: chain 'B' and resid 215 through 216 removed outlier: 4.843A pdb=" N ILE B 234 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 249 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 261 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.592A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 594 through 596 removed outlier: 3.903A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 625 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 742 through 744 removed outlier: 3.917A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 926 through 931 removed outlier: 7.221A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 949 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AC7, first strand: chain 'B' and resid 1100 through 1103 removed outlier: 3.523A pdb=" N VAL B1103 " --> pdb=" O THR B1174 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR B1174 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AC9, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD1, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.277A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.310A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 86 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.578A pdb=" N ASN C 158 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.590A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.219A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.219A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 39 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS G 118 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 116 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.099A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.558A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 208 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 136 removed outlier: 3.653A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AE3, first strand: chain 'G' and resid 235 through 237 removed outlier: 3.780A pdb=" N SER G 244 " --> pdb=" O HIS G 237 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.215A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR H 116 " --> pdb=" O MET H 123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 16 removed outlier: 6.798A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE7, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.715A pdb=" N LEU K 50 " --> pdb=" O SER K 62 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA K 61 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 105 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE K 65 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN K 102 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG K 104 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE K 88 " --> pdb=" O GLN K 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF1, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AF2, first strand: chain 'M' and resid 39 through 41 removed outlier: 3.645A pdb=" N HIS M 54 " --> pdb=" O ASP M 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AF4, first strand: chain 'M' and resid 64 through 65 Processing sheet with id=AF5, first strand: chain 'M' and resid 92 through 93 removed outlier: 3.596A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE M 81 " --> pdb=" O GLN N 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 343 through 344 removed outlier: 3.854A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE M 370 " --> pdb=" O THR M 396 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1668 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: 15.52 Time building geometry restraints manager: 16.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11849 1.33 - 1.45: 7436 1.45 - 1.58: 21002 1.58 - 1.70: 62 1.70 - 1.82: 305 Bond restraints: 40654 Sorted by residual: bond pdb=" C VAL B 121 " pdb=" N TYR B 122 " ideal model delta sigma weight residual 1.331 1.221 0.110 2.07e-02 2.33e+03 2.84e+01 bond pdb=" N ILE O 163 " pdb=" CA ILE O 163 " ideal model delta sigma weight residual 1.461 1.503 -0.042 1.31e-02 5.83e+03 1.02e+01 bond pdb=" N LEU B 476 " pdb=" CA LEU B 476 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.42e+00 bond pdb=" N LEU A 41 " pdb=" CA LEU A 41 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.98e+00 bond pdb=" N LYS A 919 " pdb=" CA LYS A 919 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.34e-02 5.57e+03 7.95e+00 ... (remaining 40649 not shown) Histogram of bond angle deviations from ideal: 96.65 - 104.17: 732 104.17 - 111.69: 16960 111.69 - 119.21: 16442 119.21 - 126.73: 20389 126.73 - 134.25: 532 Bond angle restraints: 55055 Sorted by residual: angle pdb=" C ILE O 163 " pdb=" N LEU O 164 " pdb=" CA LEU O 164 " ideal model delta sigma weight residual 120.68 133.95 -13.27 1.52e+00 4.33e-01 7.62e+01 angle pdb=" C GLU N 169 " pdb=" N HIS N 170 " pdb=" CA HIS N 170 " ideal model delta sigma weight residual 123.00 111.78 11.22 1.41e+00 5.03e-01 6.33e+01 angle pdb=" N ASN C 53 " pdb=" CA ASN C 53 " pdb=" C ASN C 53 " ideal model delta sigma weight residual 110.23 98.82 11.41 1.45e+00 4.76e-01 6.20e+01 angle pdb=" N ILE O 325 " pdb=" CA ILE O 325 " pdb=" C ILE O 325 " ideal model delta sigma weight residual 113.53 105.85 7.68 9.80e-01 1.04e+00 6.14e+01 angle pdb=" N LEU A 813 " pdb=" CA LEU A 813 " pdb=" C LEU A 813 " ideal model delta sigma weight residual 111.36 104.09 7.27 1.09e+00 8.42e-01 4.45e+01 ... (remaining 55050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 23961 29.92 - 59.83: 700 59.83 - 89.75: 61 89.75 - 119.67: 0 119.67 - 149.58: 2 Dihedral angle restraints: 24724 sinusoidal: 10378 harmonic: 14346 Sorted by residual: dihedral pdb=" C ASP B 784 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " pdb=" CB ASP B 784 " ideal model delta harmonic sigma weight residual -122.60 -138.24 15.64 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" CA ILE B 276 " pdb=" C ILE B 276 " pdb=" N LEU B 277 " pdb=" CA LEU B 277 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN B 950 " pdb=" C ASN B 950 " pdb=" N PRO B 951 " pdb=" CA PRO B 951 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 24721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5626 0.110 - 0.220: 495 0.220 - 0.331: 43 0.331 - 0.441: 5 0.441 - 0.551: 4 Chirality restraints: 6173 Sorted by residual: chirality pdb=" C3' DA U 58 " pdb=" C4' DA U 58 " pdb=" O3' DA U 58 " pdb=" C2' DA U 58 " both_signs ideal model delta sigma weight residual False -2.66 -2.11 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ASP B 784 " pdb=" N ASP B 784 " pdb=" C ASP B 784 " pdb=" CB ASP B 784 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CB ILE F 130 " pdb=" CA ILE F 130 " pdb=" CG1 ILE F 130 " pdb=" CG2 ILE F 130 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 6170 not shown) Planarity restraints: 6974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 168 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU N 168 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU N 168 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU N 169 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 617 " 0.023 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS A 617 " -0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 617 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 617 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 617 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 617 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 265 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ARG B 265 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG B 265 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 266 " 0.019 2.00e-02 2.50e+03 ... (remaining 6971 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 371 2.53 - 3.12: 28954 3.12 - 3.72: 63552 3.72 - 4.31: 85360 4.31 - 4.90: 133023 Nonbonded interactions: 311260 Sorted by model distance: nonbonded pdb=" OE2 GLU N 169 " pdb=" N HIS N 170 " model vdw 1.938 2.520 nonbonded pdb=" O TYR A1306 " pdb=" OD1 ASP A1307 " model vdw 2.000 3.040 nonbonded pdb=" OG1 THR A 64 " pdb="ZN ZN A1702 " model vdw 2.115 2.230 nonbonded pdb=" N CYS J 46 " pdb="ZN ZN J 101 " model vdw 2.159 2.310 nonbonded pdb=" OD1 ASP L 50 " pdb="ZN ZN L 101 " model vdw 2.210 2.230 ... (remaining 311255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.540 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: 0.040 Extract box with map and model: 3.480 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 103.730 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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 : 0.007 0.118 40654 Z= 0.471 Angle : 1.195 13.269 55055 Z= 0.658 Chirality : 0.069 0.551 6173 Planarity : 0.008 0.076 6974 Dihedral : 13.878 149.581 15436 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.84 % Favored : 85.02 % Rotamer: Outliers : 1.35 % Allowed : 9.60 % Favored : 89.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.09), residues: 4839 helix: -4.56 (0.07), residues: 1201 sheet: -3.47 (0.20), residues: 485 loop : -3.38 (0.09), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP B 836 HIS 0.036 0.004 HIS A 617 PHE 0.034 0.004 PHE M 364 TYR 0.045 0.004 TYR H 93 ARG 0.016 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1139 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 10 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7331 (mp0) REVERT: A 117 ARG cc_start: 0.6766 (tpm-80) cc_final: 0.5815 (tpp80) REVERT: A 136 LEU cc_start: 0.8829 (mt) cc_final: 0.8035 (mm) REVERT: A 191 MET cc_start: 0.7295 (tpp) cc_final: 0.6918 (tmm) REVERT: A 366 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6543 (ttt-90) REVERT: A 384 GLN cc_start: 0.5417 (tm-30) cc_final: 0.4845 (mt0) REVERT: A 471 MET cc_start: 0.3831 (mpt) cc_final: 0.3591 (ttp) REVERT: A 477 ASN cc_start: 0.7705 (t0) cc_final: 0.7222 (m110) REVERT: A 535 GLN cc_start: 0.6690 (mt0) cc_final: 0.6445 (mt0) REVERT: A 537 GLN cc_start: 0.7018 (pp30) cc_final: 0.6453 (mm-40) REVERT: A 549 MET cc_start: 0.6501 (mtp) cc_final: 0.6287 (mtt) REVERT: A 589 MET cc_start: 0.8601 (ttm) cc_final: 0.8306 (ttt) REVERT: A 590 ASN cc_start: 0.6591 (t0) cc_final: 0.6222 (t0) REVERT: A 596 HIS cc_start: 0.8382 (p90) cc_final: 0.7975 (p90) REVERT: A 600 MET cc_start: 0.7917 (tpp) cc_final: 0.7544 (tpp) REVERT: A 711 LYS cc_start: 0.6634 (pttp) cc_final: 0.6045 (mtmt) REVERT: A 712 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8163 (tp) REVERT: A 824 THR cc_start: 0.8162 (t) cc_final: 0.7710 (m) REVERT: A 826 PHE cc_start: 0.7622 (t80) cc_final: 0.7391 (t80) REVERT: A 833 LEU cc_start: 0.7164 (mm) cc_final: 0.6691 (mm) REVERT: A 840 ASN cc_start: 0.7848 (p0) cc_final: 0.7648 (t0) REVERT: A 880 GLN cc_start: 0.6815 (pt0) cc_final: 0.6273 (mt0) REVERT: A 981 TYR cc_start: 0.6732 (t80) cc_final: 0.5843 (t80) REVERT: A 1000 MET cc_start: 0.7707 (mmp) cc_final: 0.7294 (tpp) REVERT: A 1006 LEU cc_start: 0.7279 (pt) cc_final: 0.6884 (mp) REVERT: A 1036 ASN cc_start: 0.7478 (m-40) cc_final: 0.7000 (t0) REVERT: A 1049 MET cc_start: 0.7133 (ttm) cc_final: 0.6798 (ttm) REVERT: A 1059 LYS cc_start: 0.7226 (mttt) cc_final: 0.6728 (tptt) REVERT: A 1070 LEU cc_start: 0.8769 (tt) cc_final: 0.8533 (tp) REVERT: A 1073 TYR cc_start: 0.4979 (p90) cc_final: 0.4563 (p90) REVERT: A 1099 LYS cc_start: 0.8307 (mmpt) cc_final: 0.8074 (tmmt) REVERT: A 1248 ASP cc_start: 0.8257 (m-30) cc_final: 0.7864 (m-30) REVERT: A 1260 LYS cc_start: 0.7371 (tmmt) cc_final: 0.7088 (ttmm) REVERT: A 1269 LYS cc_start: 0.5674 (pttp) cc_final: 0.5328 (mttt) REVERT: A 1473 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6298 (mtpp) REVERT: A 1580 ARG cc_start: 0.7259 (mpp80) cc_final: 0.6008 (mtt-85) REVERT: A 1588 MET cc_start: 0.7683 (tpt) cc_final: 0.6342 (mtt) REVERT: A 1603 MET cc_start: 0.7841 (mtt) cc_final: 0.6213 (ptt) REVERT: B 90 TYR cc_start: 0.4826 (t80) cc_final: 0.4059 (m-10) REVERT: B 94 LYS cc_start: 0.5186 (tppp) cc_final: 0.4613 (tmtt) REVERT: B 100 GLU cc_start: 0.6158 (tm-30) cc_final: 0.5475 (tt0) REVERT: B 101 GLN cc_start: 0.7735 (tp40) cc_final: 0.7169 (tt0) REVERT: B 149 GLU cc_start: 0.5944 (pp20) cc_final: 0.5571 (mm-30) REVERT: B 261 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6858 (ttp80) REVERT: B 275 MET cc_start: 0.5522 (ptm) cc_final: 0.5252 (ttm) REVERT: B 290 ASP cc_start: 0.6843 (t70) cc_final: 0.6583 (t0) REVERT: B 323 ARG cc_start: 0.5857 (mpt90) cc_final: 0.3592 (ttp-170) REVERT: B 425 ILE cc_start: 0.6879 (pt) cc_final: 0.6340 (mt) REVERT: B 543 ASN cc_start: 0.7296 (p0) cc_final: 0.7074 (p0) REVERT: B 674 ILE cc_start: 0.7692 (mm) cc_final: 0.7343 (tt) REVERT: B 720 GLN cc_start: 0.8072 (mm110) cc_final: 0.6547 (tm-30) REVERT: B 726 MET cc_start: 0.7661 (ttm) cc_final: 0.7429 (ttt) REVERT: B 744 LEU cc_start: 0.7265 (tm) cc_final: 0.6887 (tm) REVERT: B 803 MET cc_start: 0.6364 (ptt) cc_final: 0.5273 (ptt) REVERT: B 822 THR cc_start: 0.3176 (p) cc_final: 0.2925 (p) REVERT: B 840 LEU cc_start: 0.6877 (mm) cc_final: 0.6622 (mp) REVERT: B 853 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6390 (tt0) REVERT: B 906 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7614 (ttp-110) REVERT: B 934 ILE cc_start: 0.7511 (mm) cc_final: 0.7119 (mm) REVERT: B 935 ASP cc_start: 0.7443 (m-30) cc_final: 0.7093 (p0) REVERT: B 974 LEU cc_start: 0.5917 (tm) cc_final: 0.5666 (tt) REVERT: B 984 TRP cc_start: 0.4866 (m100) cc_final: 0.4288 (m100) REVERT: B 1070 ARG cc_start: 0.6087 (ttt-90) cc_final: 0.4270 (tmm-80) REVERT: B 1134 ARG cc_start: 0.6680 (mmt-90) cc_final: 0.4361 (mtt180) REVERT: C 31 TRP cc_start: 0.6664 (t-100) cc_final: 0.6268 (t-100) REVERT: C 132 ILE cc_start: 0.8943 (mm) cc_final: 0.8678 (mm) REVERT: C 139 LYS cc_start: 0.8445 (mttt) cc_final: 0.8083 (mttt) REVERT: C 155 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5657 (mm-30) REVERT: C 237 GLN cc_start: 0.7055 (mt0) cc_final: 0.6604 (mp10) REVERT: C 315 PHE cc_start: 0.7854 (m-10) cc_final: 0.7521 (m-80) REVERT: C 329 LYS cc_start: 0.7588 (pptt) cc_final: 0.7297 (pptt) REVERT: D 45 ASP cc_start: 0.6819 (m-30) cc_final: 0.6209 (p0) REVERT: E 22 MET cc_start: 0.7392 (mtt) cc_final: 0.7184 (ttt) REVERT: E 34 GLU cc_start: 0.5824 (tm-30) cc_final: 0.5432 (mt-10) REVERT: E 42 PHE cc_start: 0.7719 (t80) cc_final: 0.7280 (t80) REVERT: E 61 GLN cc_start: 0.8418 (tt0) cc_final: 0.7799 (tm-30) REVERT: E 110 PHE cc_start: 0.6681 (m-10) cc_final: 0.6300 (t80) REVERT: E 208 TYR cc_start: 0.7071 (p90) cc_final: 0.6677 (p90) REVERT: F 71 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7490 (tt0) REVERT: F 76 LYS cc_start: 0.7016 (pptt) cc_final: 0.6212 (tppt) REVERT: F 77 ASP cc_start: 0.7745 (m-30) cc_final: 0.7322 (m-30) REVERT: F 99 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5789 (pp) REVERT: G 43 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6241 (pt) REVERT: G 59 GLN cc_start: 0.7072 (tt0) cc_final: 0.6407 (tt0) REVERT: G 159 LYS cc_start: 0.4032 (tttp) cc_final: 0.3652 (mmtt) REVERT: H 135 LEU cc_start: 0.6812 (pp) cc_final: 0.5916 (mt) REVERT: I 44 ASN cc_start: 0.7765 (m-40) cc_final: 0.7113 (p0) REVERT: J 49 MET cc_start: 0.8339 (mmp) cc_final: 0.8089 (mmm) REVERT: J 68 LYS cc_start: 0.7169 (tmmm) cc_final: 0.6835 (mptt) REVERT: K 57 ASP cc_start: 0.5325 (m-30) cc_final: 0.5117 (t70) REVERT: L 30 ILE cc_start: 0.7771 (mp) cc_final: 0.7563 (tp) REVERT: L 33 GLU cc_start: 0.5597 (tp30) cc_final: 0.5281 (tp30) REVERT: L 37 LYS cc_start: 0.6794 (tmtm) cc_final: 0.6552 (ttmm) REVERT: M 263 TYR cc_start: 0.5128 (t80) cc_final: 0.4583 (t80) REVERT: M 277 VAL cc_start: 0.6048 (p) cc_final: 0.5703 (t) REVERT: N 78 THR cc_start: 0.4554 (t) cc_final: 0.4150 (m) REVERT: N 88 LYS cc_start: 0.5779 (tptt) cc_final: 0.5473 (ttmt) REVERT: N 89 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3933 (mm) REVERT: O 127 GLU cc_start: 0.0593 (mt-10) cc_final: 0.0207 (tt0) REVERT: O 328 LEU cc_start: 0.2637 (mp) cc_final: 0.2235 (mt) REVERT: O 396 MET cc_start: -0.0962 (ttm) cc_final: -0.1476 (ptt) REVERT: O 467 MET cc_start: 0.2327 (mmp) cc_final: 0.1981 (mtm) outliers start: 59 outliers final: 11 residues processed: 1183 average time/residue: 0.5950 time to fit residues: 1104.2733 Evaluate side-chains 650 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 635 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 169 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.0270 chunk 369 optimal weight: 0.9980 chunk 205 optimal weight: 0.1980 chunk 126 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 232 optimal weight: 0.0980 chunk 284 optimal weight: 8.9990 chunk 443 optimal weight: 30.0000 overall best weight: 0.4640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 75 HIS A 92 ASN A 106 HIS A 116 HIS A 224 HIS A 257 ASN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 649 ASN A 693 GLN A 798 HIS A 939 ASN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1047 GLN A1072 ASN A1088 HIS ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1437 ASN A1567 ASN ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 110 ASN B 128 GLN B 168 ASN B 183 HIS B 224 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 598 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1157 GLN B1171 ASN C 323 ASN D 38 GLN E 146 HIS E 153 HIS F 104 ASN G 8 ASN G 65 HIS G 67 ASN G 126 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN G 160 ASN G 170 HIS G 235 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN K 70 HIS K 83 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 75 GLN ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN N 37 ASN N 50 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 362 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40654 Z= 0.186 Angle : 0.736 11.460 55055 Z= 0.380 Chirality : 0.046 0.273 6173 Planarity : 0.006 0.113 6974 Dihedral : 11.192 154.309 5697 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.30 % Favored : 90.64 % Rotamer: Outliers : 3.54 % Allowed : 15.81 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.10), residues: 4839 helix: -3.84 (0.09), residues: 1266 sheet: -3.11 (0.20), residues: 528 loop : -2.87 (0.10), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 836 HIS 0.011 0.001 HIS A 617 PHE 0.026 0.002 PHE O 361 TYR 0.026 0.002 TYR M 242 ARG 0.014 0.001 ARG B1130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 760 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7305 (mp0) REVERT: A 180 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6346 (mm-30) REVERT: A 191 MET cc_start: 0.7142 (tpp) cc_final: 0.6929 (tmm) REVERT: A 366 ARG cc_start: 0.6827 (ttp80) cc_final: 0.6584 (ttt-90) REVERT: A 427 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4786 (m-80) REVERT: A 471 MET cc_start: 0.4809 (mpt) cc_final: 0.4550 (mtp) REVERT: A 512 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6022 (p) REVERT: A 589 MET cc_start: 0.8477 (ttm) cc_final: 0.8164 (ttt) REVERT: A 610 ASN cc_start: 0.7080 (m-40) cc_final: 0.6649 (m-40) REVERT: A 641 GLU cc_start: 0.6263 (pp20) cc_final: 0.5524 (pm20) REVERT: A 649 ASN cc_start: 0.6739 (OUTLIER) cc_final: 0.5624 (m110) REVERT: A 712 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 768 GLU cc_start: 0.6478 (tm-30) cc_final: 0.6046 (mm-30) REVERT: A 824 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7684 (p) REVERT: A 981 TYR cc_start: 0.6020 (t80) cc_final: 0.5255 (t80) REVERT: A 1000 MET cc_start: 0.6450 (mmp) cc_final: 0.6030 (tpp) REVERT: A 1020 GLN cc_start: 0.7664 (mm110) cc_final: 0.7147 (tp-100) REVERT: A 1036 ASN cc_start: 0.7297 (m110) cc_final: 0.7072 (t0) REVERT: A 1049 MET cc_start: 0.7106 (ttm) cc_final: 0.6767 (ttm) REVERT: A 1059 LYS cc_start: 0.7092 (mttt) cc_final: 0.6853 (tptp) REVERT: A 1070 LEU cc_start: 0.8544 (tt) cc_final: 0.8182 (tp) REVERT: A 1073 TYR cc_start: 0.5501 (p90) cc_final: 0.5084 (p90) REVERT: A 1099 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7675 (pttp) REVERT: A 1150 LYS cc_start: 0.7992 (pptt) cc_final: 0.6862 (tptt) REVERT: A 1169 LEU cc_start: 0.7204 (tt) cc_final: 0.6995 (tp) REVERT: A 1225 ILE cc_start: 0.8152 (mm) cc_final: 0.7939 (tp) REVERT: A 1227 MET cc_start: 0.8742 (mtp) cc_final: 0.8217 (mtp) REVERT: A 1260 LYS cc_start: 0.7072 (tmmt) cc_final: 0.6871 (ttmm) REVERT: A 1269 LYS cc_start: 0.5694 (pttp) cc_final: 0.5050 (mttp) REVERT: A 1274 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6084 (mp0) REVERT: A 1473 LYS cc_start: 0.7129 (ttpt) cc_final: 0.6782 (mtmt) REVERT: A 1506 ARG cc_start: 0.6336 (mtp180) cc_final: 0.5807 (ptt180) REVERT: A 1588 MET cc_start: 0.7742 (tpt) cc_final: 0.6984 (mtt) REVERT: A 1591 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.5961 (ttt180) REVERT: A 1603 MET cc_start: 0.7583 (mtt) cc_final: 0.6118 (ttp) REVERT: B 73 ILE cc_start: 0.4994 (tt) cc_final: 0.4493 (mm) REVERT: B 90 TYR cc_start: 0.5231 (t80) cc_final: 0.4174 (m-10) REVERT: B 94 LYS cc_start: 0.5121 (tppp) cc_final: 0.4510 (tmtt) REVERT: B 209 GLN cc_start: 0.7549 (pp30) cc_final: 0.6990 (pp30) REVERT: B 261 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6154 (ttt-90) REVERT: B 290 ASP cc_start: 0.7409 (t70) cc_final: 0.7048 (m-30) REVERT: B 323 ARG cc_start: 0.6265 (mpt90) cc_final: 0.4108 (ttt180) REVERT: B 330 LEU cc_start: 0.6213 (mt) cc_final: 0.5996 (mt) REVERT: B 361 HIS cc_start: 0.7260 (p90) cc_final: 0.6937 (p-80) REVERT: B 411 MET cc_start: 0.6312 (mmt) cc_final: 0.5836 (mtp) REVERT: B 543 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6339 (p0) REVERT: B 614 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 672 MET cc_start: 0.7177 (ppp) cc_final: 0.6124 (ppp) REVERT: B 703 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7515 (tm) REVERT: B 720 GLN cc_start: 0.7496 (mm110) cc_final: 0.6520 (tm-30) REVERT: B 744 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6100 (tm) REVERT: B 822 THR cc_start: 0.3911 (p) cc_final: 0.3655 (p) REVERT: B 840 LEU cc_start: 0.6797 (mm) cc_final: 0.6520 (mt) REVERT: B 878 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6194 (mm-30) REVERT: B 906 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7239 (ttp80) REVERT: B 931 TRP cc_start: 0.5756 (t-100) cc_final: 0.4703 (t-100) REVERT: B 934 ILE cc_start: 0.7393 (mm) cc_final: 0.6161 (mm) REVERT: B 935 ASP cc_start: 0.7154 (m-30) cc_final: 0.6625 (p0) REVERT: B 940 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6888 (mt-10) REVERT: B 1134 ARG cc_start: 0.6804 (mmt-90) cc_final: 0.4546 (mtt180) REVERT: C 205 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7113 (ttpt) REVERT: C 329 LYS cc_start: 0.7538 (pptt) cc_final: 0.7140 (pptt) REVERT: D 45 ASP cc_start: 0.6942 (m-30) cc_final: 0.6330 (p0) REVERT: E 42 PHE cc_start: 0.7545 (t80) cc_final: 0.6837 (t80) REVERT: E 93 MET cc_start: 0.4497 (ppp) cc_final: 0.3750 (tpp) REVERT: E 110 PHE cc_start: 0.5831 (m-10) cc_final: 0.5383 (t80) REVERT: E 116 ILE cc_start: 0.5221 (OUTLIER) cc_final: 0.4678 (tp) REVERT: E 166 LYS cc_start: 0.8318 (tppp) cc_final: 0.7670 (tptt) REVERT: E 208 TYR cc_start: 0.6563 (p90) cc_final: 0.6355 (p90) REVERT: F 71 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7437 (tt0) REVERT: F 76 LYS cc_start: 0.7020 (pptt) cc_final: 0.6048 (tppt) REVERT: F 77 ASP cc_start: 0.7651 (m-30) cc_final: 0.7204 (m-30) REVERT: F 100 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7325 (tt0) REVERT: G 53 TYR cc_start: 0.6293 (m-80) cc_final: 0.6037 (m-10) REVERT: G 55 GLU cc_start: 0.6247 (tm-30) cc_final: 0.5911 (tm-30) REVERT: G 136 TYR cc_start: 0.5158 (m-10) cc_final: 0.4476 (t80) REVERT: G 159 LYS cc_start: 0.3895 (tttp) cc_final: 0.3641 (mmtt) REVERT: G 230 ARG cc_start: 0.6714 (mmm-85) cc_final: 0.6418 (tpt-90) REVERT: H 123 MET cc_start: 0.4408 (mmm) cc_final: 0.3742 (mmt) REVERT: H 135 LEU cc_start: 0.6754 (pp) cc_final: 0.5928 (mt) REVERT: I 44 ASN cc_start: 0.8010 (m-40) cc_final: 0.7226 (p0) REVERT: J 68 LYS cc_start: 0.7094 (tmmm) cc_final: 0.6712 (mptt) REVERT: K 45 GLU cc_start: 0.7731 (tp30) cc_final: 0.7211 (mt-10) REVERT: K 57 ASP cc_start: 0.5566 (m-30) cc_final: 0.5192 (t70) REVERT: K 132 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6813 (pt0) REVERT: K 142 MET cc_start: 0.6668 (tpt) cc_final: 0.5795 (tpt) REVERT: L 33 GLU cc_start: 0.5407 (tp30) cc_final: 0.4899 (tp30) REVERT: L 67 PHE cc_start: 0.5438 (m-10) cc_final: 0.4897 (m-10) REVERT: M 54 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5303 (t70) REVERT: N 74 PHE cc_start: 0.5157 (t80) cc_final: 0.4571 (p90) REVERT: N 78 THR cc_start: 0.5002 (t) cc_final: 0.4257 (m) REVERT: N 88 LYS cc_start: 0.5234 (tptt) cc_final: 0.4880 (ttmt) REVERT: O 127 GLU cc_start: 0.1481 (mt-10) cc_final: 0.1128 (tt0) REVERT: O 396 MET cc_start: -0.1813 (ttm) cc_final: -0.2348 (mmm) outliers start: 155 outliers final: 50 residues processed: 876 average time/residue: 0.5376 time to fit residues: 772.1830 Evaluate side-chains 646 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 586 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 368 optimal weight: 0.5980 chunk 301 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 443 optimal weight: 20.0000 chunk 479 optimal weight: 3.9990 chunk 395 optimal weight: 20.0000 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 356 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 336 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 686 HIS B 711 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1010 ASN B1045 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1157 GLN C 65 ASN E 147 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 126 ASN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 478 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 40654 Z= 0.328 Angle : 0.797 10.703 55055 Z= 0.411 Chirality : 0.049 0.288 6173 Planarity : 0.006 0.137 6974 Dihedral : 11.085 150.369 5682 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.04 % Favored : 86.92 % Rotamer: Outliers : 5.05 % Allowed : 18.05 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.11), residues: 4839 helix: -3.48 (0.10), residues: 1309 sheet: -2.97 (0.22), residues: 460 loop : -2.83 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 611 HIS 0.023 0.002 HIS C 216 PHE 0.021 0.002 PHE A1472 TYR 0.025 0.002 TYR A 514 ARG 0.014 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 613 time to evaluate : 4.438 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 10 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7931 (mp0) REVERT: A 191 MET cc_start: 0.7255 (tpp) cc_final: 0.6799 (tmm) REVERT: A 230 ARG cc_start: 0.3119 (OUTLIER) cc_final: 0.1239 (mtm180) REVERT: A 427 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4701 (m-80) REVERT: A 512 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6259 (p) REVERT: A 530 TRP cc_start: 0.6143 (t60) cc_final: 0.4066 (m100) REVERT: A 589 MET cc_start: 0.8474 (ttm) cc_final: 0.7806 (ttt) REVERT: A 601 MET cc_start: 0.5951 (tpt) cc_final: 0.5517 (tpt) REVERT: A 711 LYS cc_start: 0.6742 (pttp) cc_final: 0.6030 (mtmt) REVERT: A 712 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 730 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5715 (tm-30) REVERT: A 766 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 824 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8125 (m) REVERT: A 826 PHE cc_start: 0.7924 (t80) cc_final: 0.7648 (t80) REVERT: A 833 LEU cc_start: 0.7839 (mm) cc_final: 0.7608 (mm) REVERT: A 880 GLN cc_start: 0.7118 (pt0) cc_final: 0.6480 (mt0) REVERT: A 884 ARG cc_start: 0.6024 (mmp-170) cc_final: 0.5156 (ttp80) REVERT: A 1000 MET cc_start: 0.7746 (mmp) cc_final: 0.7056 (tpp) REVERT: A 1020 GLN cc_start: 0.7352 (mm110) cc_final: 0.6870 (mm110) REVERT: A 1036 ASN cc_start: 0.7870 (m110) cc_final: 0.7352 (p0) REVERT: A 1049 MET cc_start: 0.7078 (ttm) cc_final: 0.6769 (ttm) REVERT: A 1059 LYS cc_start: 0.7612 (mttt) cc_final: 0.7020 (tptm) REVERT: A 1070 LEU cc_start: 0.8615 (tt) cc_final: 0.8066 (tp) REVERT: A 1073 TYR cc_start: 0.5628 (p90) cc_final: 0.4780 (p90) REVERT: A 1099 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7673 (pttt) REVERT: A 1150 LYS cc_start: 0.8120 (pptt) cc_final: 0.6888 (tptt) REVERT: A 1192 SER cc_start: 0.9100 (m) cc_final: 0.8792 (t) REVERT: A 1225 ILE cc_start: 0.8150 (mm) cc_final: 0.7891 (tp) REVERT: A 1227 MET cc_start: 0.8897 (mtp) cc_final: 0.8288 (mtp) REVERT: A 1269 LYS cc_start: 0.5723 (pttp) cc_final: 0.5022 (mttt) REVERT: A 1439 MET cc_start: 0.5613 (mmm) cc_final: 0.5327 (mmm) REVERT: A 1473 LYS cc_start: 0.7351 (ttpt) cc_final: 0.6503 (mtpp) REVERT: A 1506 ARG cc_start: 0.6443 (mtp180) cc_final: 0.5685 (ptt180) REVERT: A 1588 MET cc_start: 0.7389 (tpt) cc_final: 0.7064 (mtm) REVERT: A 1591 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.5849 (ttt180) REVERT: A 1603 MET cc_start: 0.7868 (mtt) cc_final: 0.6459 (ttp) REVERT: B 35 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5371 (p90) REVERT: B 90 TYR cc_start: 0.5205 (t80) cc_final: 0.4311 (m-10) REVERT: B 94 LYS cc_start: 0.5336 (tppp) cc_final: 0.4590 (tmtt) REVERT: B 101 GLN cc_start: 0.8047 (tp40) cc_final: 0.7245 (tt0) REVERT: B 179 GLU cc_start: 0.6807 (tp30) cc_final: 0.5670 (tp30) REVERT: B 209 GLN cc_start: 0.7463 (pp30) cc_final: 0.7122 (pp30) REVERT: B 261 ARG cc_start: 0.7533 (ttp80) cc_final: 0.6651 (ttt-90) REVERT: B 270 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6991 (pp) REVERT: B 290 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: B 323 ARG cc_start: 0.6403 (mpt90) cc_final: 0.4012 (ttt180) REVERT: B 542 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5800 (pp) REVERT: B 543 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7010 (p0) REVERT: B 672 MET cc_start: 0.6778 (ppp) cc_final: 0.6562 (ppp) REVERT: B 673 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7560 (p0) REVERT: B 720 GLN cc_start: 0.8004 (mm110) cc_final: 0.6689 (tm-30) REVERT: B 744 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6352 (tm) REVERT: B 794 ASP cc_start: 0.8284 (t70) cc_final: 0.7856 (t0) REVERT: B 822 THR cc_start: 0.3757 (p) cc_final: 0.3473 (p) REVERT: B 839 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7155 (mttt) REVERT: B 840 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6378 (mt) REVERT: B 847 TYR cc_start: 0.5990 (m-10) cc_final: 0.5080 (m-80) REVERT: B 878 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6458 (mm-30) REVERT: B 923 GLN cc_start: 0.8458 (pp30) cc_final: 0.8177 (pp30) REVERT: B 934 ILE cc_start: 0.7874 (mm) cc_final: 0.7652 (mm) REVERT: B 1008 HIS cc_start: 0.6884 (m-70) cc_final: 0.6258 (m90) REVERT: B 1134 ARG cc_start: 0.6864 (mmt-90) cc_final: 0.4769 (mtt180) REVERT: B 1194 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5353 (mp) REVERT: C 245 ARG cc_start: 0.5794 (ppt170) cc_final: 0.5090 (tpt170) REVERT: C 314 PHE cc_start: 0.7151 (p90) cc_final: 0.6684 (p90) REVERT: C 329 LYS cc_start: 0.7508 (pptt) cc_final: 0.7267 (pptt) REVERT: D 45 ASP cc_start: 0.6918 (m-30) cc_final: 0.6339 (p0) REVERT: E 42 PHE cc_start: 0.8034 (t80) cc_final: 0.7340 (t80) REVERT: E 79 TRP cc_start: 0.7143 (t-100) cc_final: 0.6919 (t-100) REVERT: E 93 MET cc_start: 0.4255 (ppp) cc_final: 0.3815 (tpp) REVERT: E 116 ILE cc_start: 0.5331 (OUTLIER) cc_final: 0.4825 (tp) REVERT: F 76 LYS cc_start: 0.7055 (pptt) cc_final: 0.6302 (tppt) REVERT: F 77 ASP cc_start: 0.7365 (m-30) cc_final: 0.6986 (m-30) REVERT: G 30 GLU cc_start: 0.5039 (mm-30) cc_final: 0.4814 (mm-30) REVERT: G 55 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5519 (tm-30) REVERT: G 136 TYR cc_start: 0.5626 (m-10) cc_final: 0.4760 (t80) REVERT: G 159 LYS cc_start: 0.4091 (tttp) cc_final: 0.3731 (mmtt) REVERT: G 230 ARG cc_start: 0.6628 (mmm-85) cc_final: 0.6358 (tpt-90) REVERT: H 135 LEU cc_start: 0.7294 (pp) cc_final: 0.6311 (mt) REVERT: I 44 ASN cc_start: 0.8079 (m-40) cc_final: 0.7188 (p0) REVERT: J 68 LYS cc_start: 0.7132 (tmmm) cc_final: 0.6709 (mptt) REVERT: K 43 ASP cc_start: 0.6384 (p0) cc_final: 0.6142 (p0) REVERT: K 45 GLU cc_start: 0.7811 (tp30) cc_final: 0.7248 (mt-10) REVERT: K 118 GLN cc_start: 0.7352 (mm110) cc_final: 0.7123 (mm110) REVERT: K 137 GLU cc_start: 0.7757 (mp0) cc_final: 0.7453 (mp0) REVERT: L 67 PHE cc_start: 0.6246 (m-10) cc_final: 0.5502 (m-10) REVERT: M 54 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5878 (t70) REVERT: M 263 TYR cc_start: 0.4448 (t80) cc_final: 0.4023 (t80) REVERT: M 397 MET cc_start: -0.2226 (mpp) cc_final: -0.3005 (mtt) REVERT: N 40 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.3892 (mp) REVERT: N 78 THR cc_start: 0.5130 (t) cc_final: 0.4517 (m) REVERT: N 88 LYS cc_start: 0.5619 (tptt) cc_final: 0.5338 (ttmt) REVERT: O 127 GLU cc_start: 0.1802 (mt-10) cc_final: 0.1419 (tt0) REVERT: O 396 MET cc_start: -0.1611 (ttm) cc_final: -0.1935 (mmm) outliers start: 221 outliers final: 122 residues processed: 770 average time/residue: 0.5300 time to fit residues: 676.2024 Evaluate side-chains 692 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 550 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 839 LYS Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 chunk 445 optimal weight: 8.9990 chunk 471 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 422 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1503 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1114 GLN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 40654 Z= 0.307 Angle : 0.770 9.637 55055 Z= 0.397 Chirality : 0.048 0.198 6173 Planarity : 0.006 0.152 6974 Dihedral : 10.962 150.824 5678 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.16 % Favored : 86.79 % Rotamer: Outliers : 5.87 % Allowed : 19.01 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.11), residues: 4839 helix: -3.30 (0.11), residues: 1277 sheet: -2.95 (0.22), residues: 453 loop : -2.73 (0.11), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 611 HIS 0.023 0.002 HIS C 216 PHE 0.023 0.002 PHE M 132 TYR 0.026 0.002 TYR A 514 ARG 0.011 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 595 time to evaluate : 4.602 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 10 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7959 (mp0) REVERT: A 191 MET cc_start: 0.7329 (tpp) cc_final: 0.6845 (tmm) REVERT: A 230 ARG cc_start: 0.3128 (OUTLIER) cc_final: 0.1205 (mtm180) REVERT: A 427 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4353 (m-80) REVERT: A 470 HIS cc_start: 0.7714 (m-70) cc_final: 0.7348 (m-70) REVERT: A 518 GLU cc_start: 0.5979 (tp30) cc_final: 0.5649 (mm-30) REVERT: A 530 TRP cc_start: 0.6395 (t60) cc_final: 0.4181 (m100) REVERT: A 589 MET cc_start: 0.8214 (ttm) cc_final: 0.7568 (ttt) REVERT: A 600 MET cc_start: 0.8160 (tpp) cc_final: 0.7504 (tpp) REVERT: A 601 MET cc_start: 0.5804 (tpt) cc_final: 0.5129 (tpt) REVERT: A 633 MET cc_start: 0.7165 (ptp) cc_final: 0.6527 (ptp) REVERT: A 635 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6206 (tmm) REVERT: A 649 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.5533 (m110) REVERT: A 711 LYS cc_start: 0.6976 (pttp) cc_final: 0.6051 (mtmt) REVERT: A 712 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7916 (tp) REVERT: A 730 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5745 (tm-30) REVERT: A 766 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 816 LEU cc_start: 0.8462 (tm) cc_final: 0.8185 (tm) REVERT: A 817 PHE cc_start: 0.6482 (m-10) cc_final: 0.6252 (m-10) REVERT: A 818 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 824 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 826 PHE cc_start: 0.8053 (t80) cc_final: 0.7803 (t80) REVERT: A 880 GLN cc_start: 0.7109 (pt0) cc_final: 0.6427 (mt0) REVERT: A 884 ARG cc_start: 0.6025 (mmp-170) cc_final: 0.5162 (ttp80) REVERT: A 1000 MET cc_start: 0.7759 (mmp) cc_final: 0.7456 (tpp) REVERT: A 1059 LYS cc_start: 0.7783 (mttt) cc_final: 0.6941 (tptm) REVERT: A 1070 LEU cc_start: 0.8570 (tt) cc_final: 0.8188 (tp) REVERT: A 1110 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6492 (ttmt) REVERT: A 1150 LYS cc_start: 0.8089 (pptt) cc_final: 0.6814 (tptt) REVERT: A 1192 SER cc_start: 0.9092 (m) cc_final: 0.8849 (t) REVERT: A 1225 ILE cc_start: 0.8141 (mm) cc_final: 0.7848 (tp) REVERT: A 1269 LYS cc_start: 0.5567 (pttp) cc_final: 0.4953 (mttt) REVERT: A 1299 ASN cc_start: 0.6913 (t0) cc_final: 0.6535 (t0) REVERT: A 1439 MET cc_start: 0.5795 (mmm) cc_final: 0.5258 (mmm) REVERT: A 1473 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7079 (mtmt) REVERT: A 1506 ARG cc_start: 0.6566 (mtp180) cc_final: 0.5844 (ptt180) REVERT: A 1588 MET cc_start: 0.7410 (tpt) cc_final: 0.7062 (mtm) REVERT: A 1591 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.6080 (ttt180) REVERT: A 1603 MET cc_start: 0.7660 (mtt) cc_final: 0.6803 (ttp) REVERT: B 27 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 35 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5378 (p90) REVERT: B 90 TYR cc_start: 0.4803 (t80) cc_final: 0.4108 (m-10) REVERT: B 91 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7250 (pp) REVERT: B 94 LYS cc_start: 0.5667 (tppp) cc_final: 0.4541 (tmtt) REVERT: B 132 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7709 (m) REVERT: B 179 GLU cc_start: 0.6632 (tp30) cc_final: 0.5892 (tp30) REVERT: B 209 GLN cc_start: 0.7416 (pp30) cc_final: 0.7129 (pp30) REVERT: B 261 ARG cc_start: 0.7730 (ttp80) cc_final: 0.6891 (ttt-90) REVERT: B 268 GLU cc_start: 0.7349 (mp0) cc_final: 0.6991 (mp0) REVERT: B 270 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6940 (pp) REVERT: B 290 ASP cc_start: 0.7720 (t70) cc_final: 0.7147 (m-30) REVERT: B 323 ARG cc_start: 0.6530 (mpt90) cc_final: 0.3897 (ttp-170) REVERT: B 395 ASP cc_start: 0.4049 (OUTLIER) cc_final: 0.3132 (p0) REVERT: B 542 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6018 (pp) REVERT: B 543 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 672 MET cc_start: 0.6752 (ppp) cc_final: 0.6529 (ppp) REVERT: B 720 GLN cc_start: 0.8371 (mm110) cc_final: 0.6845 (tm-30) REVERT: B 742 TYR cc_start: 0.7742 (m-10) cc_final: 0.7521 (m-80) REVERT: B 743 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.5890 (ttp80) REVERT: B 744 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6350 (tm) REVERT: B 794 ASP cc_start: 0.8271 (t70) cc_final: 0.7794 (t0) REVERT: B 822 THR cc_start: 0.3929 (p) cc_final: 0.3590 (p) REVERT: B 839 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7379 (mttt) REVERT: B 840 LEU cc_start: 0.6807 (mm) cc_final: 0.6341 (mt) REVERT: B 847 TYR cc_start: 0.5572 (m-10) cc_final: 0.4830 (m-80) REVERT: B 878 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6599 (mm-30) REVERT: B 923 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7872 (pp30) REVERT: B 1134 ARG cc_start: 0.6865 (mmt-90) cc_final: 0.4607 (mtt180) REVERT: B 1194 ILE cc_start: 0.5880 (OUTLIER) cc_final: 0.5602 (mp) REVERT: C 68 ARG cc_start: 0.7351 (ttp80) cc_final: 0.7130 (ttt-90) REVERT: C 174 ARG cc_start: 0.6843 (tmm160) cc_final: 0.6552 (tmm-80) REVERT: C 245 ARG cc_start: 0.5604 (ppt170) cc_final: 0.5014 (tpt170) REVERT: C 295 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7683 (mmm160) REVERT: C 314 PHE cc_start: 0.6896 (p90) cc_final: 0.6299 (p90) REVERT: C 329 LYS cc_start: 0.7467 (pptt) cc_final: 0.6642 (pptt) REVERT: D 39 PHE cc_start: 0.5034 (m-80) cc_final: 0.4705 (m-80) REVERT: D 45 ASP cc_start: 0.6930 (m-30) cc_final: 0.6491 (p0) REVERT: E 42 PHE cc_start: 0.8073 (t80) cc_final: 0.7430 (t80) REVERT: E 79 TRP cc_start: 0.7184 (t-100) cc_final: 0.6781 (t-100) REVERT: E 93 MET cc_start: 0.4177 (ppp) cc_final: 0.3777 (tpp) REVERT: E 116 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5026 (tp) REVERT: E 149 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6250 (mm) REVERT: E 160 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: E 171 LYS cc_start: 0.5046 (mmtt) cc_final: 0.4805 (mmtt) REVERT: E 177 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.5736 (ppt-90) REVERT: F 76 LYS cc_start: 0.6945 (pptt) cc_final: 0.6135 (tppt) REVERT: F 77 ASP cc_start: 0.7367 (m-30) cc_final: 0.7023 (m-30) REVERT: F 103 MET cc_start: 0.5008 (mmt) cc_final: 0.4494 (mmt) REVERT: F 120 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5148 (mt) REVERT: G 76 LYS cc_start: 0.6828 (tptt) cc_final: 0.6529 (tptp) REVERT: G 136 TYR cc_start: 0.5673 (m-10) cc_final: 0.4829 (t80) REVERT: G 159 LYS cc_start: 0.4084 (tttp) cc_final: 0.3760 (mmtt) REVERT: I 44 ASN cc_start: 0.8136 (m-40) cc_final: 0.7188 (p0) REVERT: J 68 LYS cc_start: 0.7013 (tmmm) cc_final: 0.6591 (mptt) REVERT: K 43 ASP cc_start: 0.6540 (p0) cc_final: 0.6080 (p0) REVERT: K 45 GLU cc_start: 0.7622 (tp30) cc_final: 0.7230 (mt-10) REVERT: K 137 GLU cc_start: 0.7195 (mp0) cc_final: 0.6942 (mp0) REVERT: L 38 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.4122 (pp) REVERT: L 67 PHE cc_start: 0.6240 (m-10) cc_final: 0.5513 (m-10) REVERT: M 54 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5714 (t70) REVERT: M 178 LEU cc_start: 0.5303 (OUTLIER) cc_final: 0.4031 (mt) REVERT: M 263 TYR cc_start: 0.4458 (t80) cc_final: 0.4058 (t80) REVERT: M 397 MET cc_start: -0.2053 (mpp) cc_final: -0.2728 (mtt) REVERT: N 40 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.3971 (mp) REVERT: N 78 THR cc_start: 0.5230 (t) cc_final: 0.4418 (m) REVERT: N 88 LYS cc_start: 0.5666 (tptt) cc_final: 0.5347 (ttmt) REVERT: N 107 MET cc_start: 0.6870 (mpp) cc_final: 0.6532 (mpp) REVERT: O 127 GLU cc_start: 0.2149 (mt-10) cc_final: 0.1681 (tt0) REVERT: O 385 MET cc_start: -0.2293 (mpp) cc_final: -0.2507 (mpp) REVERT: O 396 MET cc_start: -0.1408 (ttm) cc_final: -0.1650 (mmm) outliers start: 257 outliers final: 148 residues processed: 787 average time/residue: 0.5151 time to fit residues: 675.8417 Evaluate side-chains 715 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 535 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1110 LYS Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 743 ARG Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 839 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 6 optimal weight: 0.3980 chunk 351 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 402 optimal weight: 0.9980 chunk 326 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 423 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 257 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 54 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 40654 Z= 0.224 Angle : 0.703 9.562 55055 Z= 0.360 Chirality : 0.046 0.215 6173 Planarity : 0.005 0.132 6974 Dihedral : 10.687 151.181 5678 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.32 % Favored : 87.64 % Rotamer: Outliers : 5.69 % Allowed : 20.20 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.11), residues: 4839 helix: -3.10 (0.12), residues: 1288 sheet: -2.88 (0.21), residues: 485 loop : -2.59 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 143 HIS 0.016 0.001 HIS C 216 PHE 0.029 0.002 PHE M 132 TYR 0.039 0.002 TYR B1198 ARG 0.008 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 570 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7844 (mp0) REVERT: A 64 THR cc_start: 0.2358 (OUTLIER) cc_final: 0.2090 (p) REVERT: A 191 MET cc_start: 0.7331 (tpp) cc_final: 0.6844 (tmm) REVERT: A 230 ARG cc_start: 0.2845 (OUTLIER) cc_final: 0.1085 (mtm180) REVERT: A 427 PHE cc_start: 0.3964 (OUTLIER) cc_final: 0.3729 (m-80) REVERT: A 470 HIS cc_start: 0.7632 (m-70) cc_final: 0.7374 (m-70) REVERT: A 530 TRP cc_start: 0.6386 (t60) cc_final: 0.4164 (m100) REVERT: A 589 MET cc_start: 0.8634 (ttm) cc_final: 0.8012 (ttt) REVERT: A 590 ASN cc_start: 0.7959 (m-40) cc_final: 0.7666 (m110) REVERT: A 601 MET cc_start: 0.5672 (tpt) cc_final: 0.5202 (tpt) REVERT: A 632 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7267 (pp20) REVERT: A 633 MET cc_start: 0.6967 (ptp) cc_final: 0.6223 (ptp) REVERT: A 635 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6318 (tmm) REVERT: A 641 GLU cc_start: 0.6192 (pp20) cc_final: 0.5484 (pm20) REVERT: A 667 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6433 (mtp180) REVERT: A 712 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 730 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: A 824 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8383 (m) REVERT: A 884 ARG cc_start: 0.5988 (mmp-170) cc_final: 0.5238 (ttp80) REVERT: A 892 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5611 (pp) REVERT: A 953 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5952 (pp20) REVERT: A 1059 LYS cc_start: 0.7708 (mttt) cc_final: 0.6889 (tptp) REVERT: A 1089 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.6027 (mm) REVERT: A 1110 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6488 (tttt) REVERT: A 1145 GLU cc_start: 0.7883 (tp30) cc_final: 0.7597 (tp30) REVERT: A 1150 LYS cc_start: 0.8071 (pptt) cc_final: 0.6816 (tptt) REVERT: A 1225 ILE cc_start: 0.8138 (mm) cc_final: 0.7840 (tp) REVERT: A 1269 LYS cc_start: 0.5547 (pttp) cc_final: 0.4870 (mttt) REVERT: A 1299 ASN cc_start: 0.6893 (t0) cc_final: 0.6331 (m-40) REVERT: A 1439 MET cc_start: 0.5845 (mmm) cc_final: 0.5390 (mmm) REVERT: A 1473 LYS cc_start: 0.7431 (ttpt) cc_final: 0.7040 (mtmt) REVERT: A 1506 ARG cc_start: 0.6554 (mtp180) cc_final: 0.5827 (ptt180) REVERT: A 1588 MET cc_start: 0.7352 (tpt) cc_final: 0.7035 (mtm) REVERT: A 1591 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6303 (ttt180) REVERT: A 1603 MET cc_start: 0.7446 (mtt) cc_final: 0.6393 (ttp) REVERT: A 1604 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: B 35 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5376 (p90) REVERT: B 90 TYR cc_start: 0.4916 (t80) cc_final: 0.4238 (m-10) REVERT: B 132 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7676 (m) REVERT: B 175 MET cc_start: 0.6969 (tpp) cc_final: 0.6677 (tpp) REVERT: B 206 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6983 (tm) REVERT: B 209 GLN cc_start: 0.7310 (pp30) cc_final: 0.7078 (pp30) REVERT: B 261 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6709 (ttt-90) REVERT: B 264 TRP cc_start: 0.6430 (t-100) cc_final: 0.6224 (t-100) REVERT: B 268 GLU cc_start: 0.7350 (mp0) cc_final: 0.6806 (mp0) REVERT: B 270 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6879 (pp) REVERT: B 290 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: B 323 ARG cc_start: 0.6494 (mpt90) cc_final: 0.3847 (ttp-170) REVERT: B 362 LEU cc_start: 0.8402 (mt) cc_final: 0.8164 (tt) REVERT: B 395 ASP cc_start: 0.4264 (OUTLIER) cc_final: 0.3455 (p0) REVERT: B 425 ILE cc_start: 0.6640 (pt) cc_final: 0.6126 (tt) REVERT: B 543 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7146 (p0) REVERT: B 681 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 720 GLN cc_start: 0.8296 (mm110) cc_final: 0.6961 (tm-30) REVERT: B 742 TYR cc_start: 0.7714 (m-10) cc_final: 0.7497 (m-80) REVERT: B 744 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6032 (tm) REVERT: B 794 ASP cc_start: 0.8190 (t70) cc_final: 0.7779 (t0) REVERT: B 822 THR cc_start: 0.4192 (p) cc_final: 0.3838 (p) REVERT: B 839 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7351 (mttt) REVERT: B 840 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6601 (mt) REVERT: B 847 TYR cc_start: 0.5898 (m-10) cc_final: 0.5325 (m-80) REVERT: B 878 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 882 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5926 (mt) REVERT: B 923 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7893 (pp30) REVERT: B 957 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.6901 (mmm-85) REVERT: B 958 MET cc_start: 0.6996 (tmm) cc_final: 0.6779 (tmm) REVERT: B 1134 ARG cc_start: 0.6776 (mmt-90) cc_final: 0.4615 (mtt180) REVERT: B 1166 LYS cc_start: 0.6524 (tppt) cc_final: 0.6224 (tttm) REVERT: C 34 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.4515 (tm-30) REVERT: C 68 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7159 (ttt-90) REVERT: C 174 ARG cc_start: 0.6783 (tmm160) cc_final: 0.6580 (tmm-80) REVERT: C 245 ARG cc_start: 0.5660 (ppt170) cc_final: 0.5181 (tpt170) REVERT: C 295 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7656 (mmm160) REVERT: C 314 PHE cc_start: 0.6886 (p90) cc_final: 0.6218 (p90) REVERT: C 329 LYS cc_start: 0.7531 (pptt) cc_final: 0.6541 (pptt) REVERT: D 39 PHE cc_start: 0.5019 (m-80) cc_final: 0.4701 (m-80) REVERT: D 45 ASP cc_start: 0.6904 (m-30) cc_final: 0.6469 (p0) REVERT: E 42 PHE cc_start: 0.7868 (t80) cc_final: 0.7200 (t80) REVERT: E 79 TRP cc_start: 0.7126 (t-100) cc_final: 0.6859 (t-100) REVERT: E 93 MET cc_start: 0.4063 (ppp) cc_final: 0.3731 (tpp) REVERT: E 116 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5352 (tp) REVERT: E 149 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6369 (mm) REVERT: E 171 LYS cc_start: 0.5111 (mmtt) cc_final: 0.4859 (mmtt) REVERT: E 177 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.4902 (ppt-90) REVERT: E 215 MET cc_start: 0.3624 (pp-130) cc_final: 0.3115 (pp-130) REVERT: F 103 MET cc_start: 0.5296 (mmt) cc_final: 0.5006 (mmt) REVERT: G 55 GLU cc_start: 0.6278 (tm-30) cc_final: 0.6034 (tm-30) REVERT: G 76 LYS cc_start: 0.6700 (tptt) cc_final: 0.5857 (mttt) REVERT: G 136 TYR cc_start: 0.5657 (m-10) cc_final: 0.4809 (t80) REVERT: G 159 LYS cc_start: 0.4182 (tttp) cc_final: 0.3827 (mmtt) REVERT: H 98 TYR cc_start: 0.6921 (t80) cc_final: 0.6616 (t80) REVERT: I 44 ASN cc_start: 0.7876 (m-40) cc_final: 0.6888 (p0) REVERT: J 68 LYS cc_start: 0.7023 (tmmm) cc_final: 0.6572 (mptt) REVERT: K 43 ASP cc_start: 0.6639 (p0) cc_final: 0.6090 (p0) REVERT: K 45 GLU cc_start: 0.7552 (tp30) cc_final: 0.7255 (mt-10) REVERT: K 91 TYR cc_start: 0.8383 (p90) cc_final: 0.7883 (p90) REVERT: K 118 GLN cc_start: 0.7174 (mm110) cc_final: 0.6577 (mm110) REVERT: K 137 GLU cc_start: 0.7173 (mp0) cc_final: 0.6940 (mp0) REVERT: L 38 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.3930 (pp) REVERT: L 67 PHE cc_start: 0.6002 (m-10) cc_final: 0.5464 (m-10) REVERT: M 54 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5072 (t70) REVERT: M 178 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.3703 (mt) REVERT: M 263 TYR cc_start: 0.4464 (t80) cc_final: 0.4047 (t80) REVERT: M 397 MET cc_start: -0.2439 (mpp) cc_final: -0.3035 (mtt) REVERT: N 40 LEU cc_start: 0.4269 (OUTLIER) cc_final: 0.3740 (mp) REVERT: O 396 MET cc_start: -0.1445 (ttm) cc_final: -0.1681 (ptm) REVERT: O 606 MET cc_start: -0.2275 (tmm) cc_final: -0.2533 (tmm) outliers start: 249 outliers final: 141 residues processed: 753 average time/residue: 0.5777 time to fit residues: 726.5268 Evaluate side-chains 708 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 531 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1110 LYS Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 839 LYS Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 472 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 156 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 216 HIS ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN O 117 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40654 Z= 0.211 Angle : 0.691 14.489 55055 Z= 0.350 Chirality : 0.045 0.198 6173 Planarity : 0.005 0.122 6974 Dihedral : 10.494 151.181 5678 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.84 % Favored : 88.12 % Rotamer: Outliers : 5.71 % Allowed : 21.02 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.11), residues: 4839 helix: -2.96 (0.12), residues: 1305 sheet: -2.65 (0.22), residues: 470 loop : -2.55 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 611 HIS 0.016 0.001 HIS C 216 PHE 0.027 0.002 PHE M 132 TYR 0.021 0.002 TYR J 21 ARG 0.006 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 554 time to evaluate : 4.868 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 10 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7864 (mp0) REVERT: A 64 THR cc_start: 0.2311 (OUTLIER) cc_final: 0.2048 (p) REVERT: A 191 MET cc_start: 0.7373 (tpp) cc_final: 0.6865 (tmm) REVERT: A 230 ARG cc_start: 0.3073 (OUTLIER) cc_final: 0.1326 (mtm180) REVERT: A 470 HIS cc_start: 0.7697 (m-70) cc_final: 0.7394 (m-70) REVERT: A 494 GLU cc_start: 0.5448 (mt-10) cc_final: 0.5223 (mt-10) REVERT: A 518 GLU cc_start: 0.5783 (tp30) cc_final: 0.5435 (mm-30) REVERT: A 530 TRP cc_start: 0.6368 (t60) cc_final: 0.4160 (m100) REVERT: A 589 MET cc_start: 0.8742 (ttm) cc_final: 0.8124 (ttt) REVERT: A 601 MET cc_start: 0.5568 (tpt) cc_final: 0.5070 (tpt) REVERT: A 610 ASN cc_start: 0.6867 (m-40) cc_final: 0.6458 (m-40) REVERT: A 632 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7321 (pp20) REVERT: A 633 MET cc_start: 0.6978 (ptp) cc_final: 0.6432 (ptp) REVERT: A 635 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6163 (tmm) REVERT: A 641 GLU cc_start: 0.6308 (pp20) cc_final: 0.5639 (pm20) REVERT: A 667 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6434 (mtp180) REVERT: A 730 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: A 884 ARG cc_start: 0.6022 (mmp-170) cc_final: 0.5225 (ttp80) REVERT: A 953 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5784 (pp20) REVERT: A 1059 LYS cc_start: 0.7687 (mttt) cc_final: 0.6880 (tptp) REVERT: A 1110 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6575 (tttt) REVERT: A 1145 GLU cc_start: 0.7910 (tp30) cc_final: 0.7611 (tp30) REVERT: A 1150 LYS cc_start: 0.8004 (pptt) cc_final: 0.6776 (tptt) REVERT: A 1225 ILE cc_start: 0.8128 (mm) cc_final: 0.7832 (tp) REVERT: A 1269 LYS cc_start: 0.5655 (pttp) cc_final: 0.5330 (ttmt) REVERT: A 1299 ASN cc_start: 0.6892 (t0) cc_final: 0.6336 (m-40) REVERT: A 1439 MET cc_start: 0.5811 (mmm) cc_final: 0.5288 (mmm) REVERT: A 1473 LYS cc_start: 0.7441 (ttpt) cc_final: 0.7044 (mtmt) REVERT: A 1506 ARG cc_start: 0.6581 (mtp180) cc_final: 0.5823 (ptt180) REVERT: A 1588 MET cc_start: 0.7333 (tpt) cc_final: 0.6996 (mtm) REVERT: A 1591 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6335 (ttt180) REVERT: A 1603 MET cc_start: 0.7424 (mtt) cc_final: 0.6366 (ttp) REVERT: A 1604 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: A 1620 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: A 1662 ASN cc_start: 0.4582 (OUTLIER) cc_final: 0.4382 (p0) REVERT: B 27 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8086 (p0) REVERT: B 35 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5311 (p90) REVERT: B 90 TYR cc_start: 0.5134 (t80) cc_final: 0.4350 (m-10) REVERT: B 132 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7716 (m) REVERT: B 206 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6966 (tm) REVERT: B 209 GLN cc_start: 0.7265 (pp30) cc_final: 0.7052 (pp30) REVERT: B 261 ARG cc_start: 0.7385 (ttp80) cc_final: 0.6657 (ttt-90) REVERT: B 264 TRP cc_start: 0.6567 (t-100) cc_final: 0.6252 (t-100) REVERT: B 268 GLU cc_start: 0.7038 (mp0) cc_final: 0.6609 (mp0) REVERT: B 270 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6902 (pp) REVERT: B 290 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: B 323 ARG cc_start: 0.6620 (mpt90) cc_final: 0.3850 (ttp-170) REVERT: B 395 ASP cc_start: 0.4270 (OUTLIER) cc_final: 0.3392 (p0) REVERT: B 411 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: B 425 ILE cc_start: 0.6609 (pt) cc_final: 0.6066 (tt) REVERT: B 543 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7283 (p0) REVERT: B 623 ASP cc_start: 0.4008 (OUTLIER) cc_final: 0.3271 (m-30) REVERT: B 672 MET cc_start: 0.6701 (ppp) cc_final: 0.6188 (ptt) REVERT: B 681 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 720 GLN cc_start: 0.8108 (mm110) cc_final: 0.7651 (tp-100) REVERT: B 743 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.5955 (ttp80) REVERT: B 744 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6083 (tm) REVERT: B 790 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: B 822 THR cc_start: 0.3834 (p) cc_final: 0.3474 (p) REVERT: B 882 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6202 (mt) REVERT: B 923 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7708 (pp30) REVERT: B 957 ARG cc_start: 0.7213 (mmt-90) cc_final: 0.6909 (mmm-85) REVERT: B 1013 MET cc_start: 0.7208 (mtp) cc_final: 0.6909 (ptp) REVERT: B 1126 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6107 (m) REVERT: B 1134 ARG cc_start: 0.6757 (mmt-90) cc_final: 0.4597 (mtt180) REVERT: B 1166 LYS cc_start: 0.6504 (tppt) cc_final: 0.6206 (tttm) REVERT: B 1192 MET cc_start: 0.6611 (ptt) cc_final: 0.6166 (tpt) REVERT: C 34 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4625 (tm-30) REVERT: C 68 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7235 (ttt-90) REVERT: C 174 ARG cc_start: 0.6711 (tmm160) cc_final: 0.6511 (tmm-80) REVERT: C 245 ARG cc_start: 0.5678 (ppt170) cc_final: 0.5098 (tpt170) REVERT: C 314 PHE cc_start: 0.6852 (p90) cc_final: 0.6138 (p90) REVERT: C 329 LYS cc_start: 0.7600 (pptt) cc_final: 0.6634 (pptt) REVERT: D 38 GLN cc_start: 0.4833 (mp10) cc_final: 0.4596 (pm20) REVERT: D 39 PHE cc_start: 0.5025 (m-80) cc_final: 0.4631 (m-80) REVERT: D 45 ASP cc_start: 0.6889 (m-30) cc_final: 0.6359 (p0) REVERT: D 90 LYS cc_start: 0.4251 (mmtt) cc_final: 0.4048 (mmtt) REVERT: D 91 ARG cc_start: 0.3532 (OUTLIER) cc_final: 0.2759 (mtt180) REVERT: E 42 PHE cc_start: 0.7823 (t80) cc_final: 0.7037 (t80) REVERT: E 79 TRP cc_start: 0.7090 (t-100) cc_final: 0.6754 (t-100) REVERT: E 93 MET cc_start: 0.3943 (ppp) cc_final: 0.3585 (tpp) REVERT: E 116 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5369 (tp) REVERT: E 149 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6486 (mm) REVERT: E 171 LYS cc_start: 0.5252 (mmtt) cc_final: 0.5032 (mmtt) REVERT: E 177 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5856 (ptt-90) REVERT: E 215 MET cc_start: 0.3537 (pp-130) cc_final: 0.3312 (pp-130) REVERT: F 120 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4748 (mt) REVERT: G 55 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5877 (tm-30) REVERT: G 76 LYS cc_start: 0.6586 (tptt) cc_final: 0.6315 (tptp) REVERT: G 107 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6492 (tt) REVERT: G 136 TYR cc_start: 0.5855 (m-10) cc_final: 0.5015 (t80) REVERT: G 159 LYS cc_start: 0.4679 (tttp) cc_final: 0.4411 (mmtt) REVERT: H 98 TYR cc_start: 0.6972 (t80) cc_final: 0.6722 (t80) REVERT: I 44 ASN cc_start: 0.7784 (m-40) cc_final: 0.6798 (p0) REVERT: J 68 LYS cc_start: 0.6993 (tmmm) cc_final: 0.6568 (mptt) REVERT: K 43 ASP cc_start: 0.6734 (p0) cc_final: 0.6101 (p0) REVERT: K 45 GLU cc_start: 0.7547 (tp30) cc_final: 0.7271 (mt-10) REVERT: K 91 TYR cc_start: 0.8358 (p90) cc_final: 0.7965 (p90) REVERT: K 118 GLN cc_start: 0.7170 (mm110) cc_final: 0.6580 (mm110) REVERT: K 137 GLU cc_start: 0.7163 (mp0) cc_final: 0.6942 (mp0) REVERT: L 38 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.4148 (pp) REVERT: L 67 PHE cc_start: 0.5975 (m-10) cc_final: 0.5602 (m-10) REVERT: M 54 HIS cc_start: 0.5865 (OUTLIER) cc_final: 0.5272 (t70) REVERT: M 178 LEU cc_start: 0.4016 (OUTLIER) cc_final: 0.3096 (mt) REVERT: M 263 TYR cc_start: 0.4583 (t80) cc_final: 0.4149 (t80) REVERT: M 397 MET cc_start: -0.2444 (mpp) cc_final: -0.2994 (mtt) REVERT: N 40 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3719 (mp) outliers start: 250 outliers final: 158 residues processed: 740 average time/residue: 0.5308 time to fit residues: 657.2241 Evaluate side-chains 725 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 527 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1110 LYS Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain A residue 1662 ASN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 743 ARG Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 790 ASN Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 397 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 470 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS A1293 HIS A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 207 HIS ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40654 Z= 0.230 Angle : 0.698 12.555 55055 Z= 0.354 Chirality : 0.046 0.182 6173 Planarity : 0.005 0.122 6974 Dihedral : 10.434 150.880 5676 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.79 % Favored : 87.17 % Rotamer: Outliers : 5.96 % Allowed : 21.48 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 4839 helix: -2.85 (0.12), residues: 1292 sheet: -2.65 (0.22), residues: 480 loop : -2.51 (0.11), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 611 HIS 0.013 0.001 HIS A 617 PHE 0.027 0.002 PHE M 132 TYR 0.030 0.002 TYR B 742 ARG 0.005 0.001 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 558 time to evaluate : 5.072 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 10 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7634 (mp0) REVERT: A 191 MET cc_start: 0.7382 (tpp) cc_final: 0.6858 (tmm) REVERT: A 230 ARG cc_start: 0.3066 (OUTLIER) cc_final: 0.1355 (mtm180) REVERT: A 470 HIS cc_start: 0.7820 (m-70) cc_final: 0.7494 (m-70) REVERT: A 518 GLU cc_start: 0.5788 (tp30) cc_final: 0.5425 (mm-30) REVERT: A 530 TRP cc_start: 0.6323 (t60) cc_final: 0.4130 (m100) REVERT: A 601 MET cc_start: 0.5569 (tpt) cc_final: 0.4871 (tpt) REVERT: A 610 ASN cc_start: 0.6949 (m-40) cc_final: 0.6612 (m-40) REVERT: A 632 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: A 633 MET cc_start: 0.7211 (ptp) cc_final: 0.6516 (ptp) REVERT: A 635 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6192 (tmm) REVERT: A 641 GLU cc_start: 0.6216 (pp20) cc_final: 0.5713 (pm20) REVERT: A 667 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6505 (mtp180) REVERT: A 711 LYS cc_start: 0.6690 (pttp) cc_final: 0.5951 (mtmt) REVERT: A 730 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6336 (tm-30) REVERT: A 811 SER cc_start: 0.7791 (m) cc_final: 0.7531 (p) REVERT: A 884 ARG cc_start: 0.5955 (mmp-170) cc_final: 0.5141 (ttp80) REVERT: A 892 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5602 (pp) REVERT: A 953 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5773 (pp20) REVERT: A 1059 LYS cc_start: 0.7707 (mttt) cc_final: 0.6876 (tptp) REVERT: A 1073 TYR cc_start: 0.5437 (p90) cc_final: 0.5075 (p90) REVERT: A 1110 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6619 (tttt) REVERT: A 1145 GLU cc_start: 0.7870 (tp30) cc_final: 0.7517 (tp30) REVERT: A 1150 LYS cc_start: 0.8023 (pptt) cc_final: 0.6831 (tptt) REVERT: A 1225 ILE cc_start: 0.8117 (mm) cc_final: 0.7808 (tp) REVERT: A 1269 LYS cc_start: 0.5674 (pttp) cc_final: 0.5337 (ttmt) REVERT: A 1299 ASN cc_start: 0.6962 (t0) cc_final: 0.6636 (t0) REVERT: A 1439 MET cc_start: 0.5769 (mmm) cc_final: 0.5227 (mmm) REVERT: A 1473 LYS cc_start: 0.7403 (ttpt) cc_final: 0.7054 (mtmt) REVERT: A 1506 ARG cc_start: 0.6504 (mtp180) cc_final: 0.5703 (ptt180) REVERT: A 1579 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: A 1588 MET cc_start: 0.7393 (tpt) cc_final: 0.6991 (mtm) REVERT: A 1591 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.6304 (ttt180) REVERT: A 1603 MET cc_start: 0.7425 (mtt) cc_final: 0.6417 (ttp) REVERT: A 1620 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6826 (mp10) REVERT: B 27 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8065 (p0) REVERT: B 35 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5353 (p90) REVERT: B 90 TYR cc_start: 0.5156 (t80) cc_final: 0.4364 (m-10) REVERT: B 132 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7732 (m) REVERT: B 206 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7038 (tm) REVERT: B 261 ARG cc_start: 0.7444 (ttp80) cc_final: 0.6767 (ttt-90) REVERT: B 270 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6906 (pp) REVERT: B 290 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: B 323 ARG cc_start: 0.6540 (mpt90) cc_final: 0.3869 (ttp-170) REVERT: B 395 ASP cc_start: 0.4285 (OUTLIER) cc_final: 0.3338 (p0) REVERT: B 411 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7165 (mpp) REVERT: B 425 ILE cc_start: 0.6385 (pt) cc_final: 0.5799 (tt) REVERT: B 623 ASP cc_start: 0.3909 (OUTLIER) cc_final: 0.3068 (m-30) REVERT: B 672 MET cc_start: 0.6698 (ppp) cc_final: 0.6223 (ptt) REVERT: B 681 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8337 (mt) REVERT: B 720 GLN cc_start: 0.8149 (mm110) cc_final: 0.7755 (tp40) REVERT: B 743 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.5993 (ttp80) REVERT: B 744 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6107 (tm) REVERT: B 790 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.6873 (m-40) REVERT: B 822 THR cc_start: 0.3905 (p) cc_final: 0.3534 (p) REVERT: B 847 TYR cc_start: 0.6044 (m-10) cc_final: 0.5512 (m-80) REVERT: B 882 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6331 (mt) REVERT: B 923 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: B 940 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6394 (pm20) REVERT: B 957 ARG cc_start: 0.7084 (mmt-90) cc_final: 0.6688 (mmm-85) REVERT: B 1013 MET cc_start: 0.7294 (mtp) cc_final: 0.7068 (mtp) REVERT: B 1126 VAL cc_start: 0.6427 (OUTLIER) cc_final: 0.6022 (m) REVERT: B 1133 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6658 (mtm) REVERT: B 1134 ARG cc_start: 0.6824 (mmt-90) cc_final: 0.4524 (mtt180) REVERT: B 1166 LYS cc_start: 0.6932 (tppt) cc_final: 0.6601 (tttm) REVERT: B 1192 MET cc_start: 0.6592 (ptt) cc_final: 0.6195 (tpt) REVERT: C 34 GLU cc_start: 0.5279 (OUTLIER) cc_final: 0.4640 (tm-30) REVERT: C 245 ARG cc_start: 0.5680 (ppt170) cc_final: 0.5122 (tpt170) REVERT: C 314 PHE cc_start: 0.6881 (p90) cc_final: 0.6178 (p90) REVERT: C 329 LYS cc_start: 0.7589 (pptt) cc_final: 0.6692 (pptt) REVERT: D 38 GLN cc_start: 0.4938 (mp10) cc_final: 0.4723 (pm20) REVERT: D 39 PHE cc_start: 0.5364 (m-80) cc_final: 0.4903 (m-80) REVERT: D 45 ASP cc_start: 0.6868 (m-30) cc_final: 0.6354 (p0) REVERT: D 91 ARG cc_start: 0.3543 (OUTLIER) cc_final: 0.2772 (mtt180) REVERT: E 42 PHE cc_start: 0.7678 (t80) cc_final: 0.6976 (t80) REVERT: E 79 TRP cc_start: 0.7137 (t-100) cc_final: 0.6825 (t-100) REVERT: E 93 MET cc_start: 0.4345 (ppp) cc_final: 0.3434 (tpp) REVERT: E 116 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5398 (tp) REVERT: E 149 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6369 (mm) REVERT: E 171 LYS cc_start: 0.5150 (mmtt) cc_final: 0.4729 (mmtt) REVERT: E 177 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.5777 (ptt-90) REVERT: F 85 MET cc_start: 0.7360 (tpt) cc_final: 0.7128 (tpt) REVERT: F 120 ILE cc_start: 0.5211 (OUTLIER) cc_final: 0.4983 (mt) REVERT: G 55 GLU cc_start: 0.6172 (tm-30) cc_final: 0.5848 (tm-30) REVERT: G 107 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6548 (tt) REVERT: G 136 TYR cc_start: 0.5850 (m-10) cc_final: 0.5013 (t80) REVERT: G 159 LYS cc_start: 0.4813 (tttp) cc_final: 0.4527 (mmtt) REVERT: H 45 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: H 98 TYR cc_start: 0.7007 (t80) cc_final: 0.6668 (t80) REVERT: I 44 ASN cc_start: 0.7774 (m-40) cc_final: 0.6781 (p0) REVERT: J 68 LYS cc_start: 0.7004 (tmmm) cc_final: 0.6579 (mptt) REVERT: K 43 ASP cc_start: 0.6993 (p0) cc_final: 0.6354 (p0) REVERT: K 91 TYR cc_start: 0.8257 (p90) cc_final: 0.7988 (p90) REVERT: L 38 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.4148 (pp) REVERT: L 67 PHE cc_start: 0.5963 (m-10) cc_final: 0.5454 (m-10) REVERT: M 54 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.4808 (t70) REVERT: M 178 LEU cc_start: 0.4021 (OUTLIER) cc_final: 0.3121 (mt) REVERT: M 263 TYR cc_start: 0.4588 (t80) cc_final: 0.4180 (t80) REVERT: M 397 MET cc_start: -0.2477 (mpp) cc_final: -0.3016 (mtt) REVERT: N 40 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3564 (mp) outliers start: 261 outliers final: 173 residues processed: 749 average time/residue: 0.5760 time to fit residues: 731.8509 Evaluate side-chains 736 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 523 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1110 LYS Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1579 PHE Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1620 GLN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 743 ARG Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 790 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 347 THR Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 454 VAL Chi-restraints excluded: chain O residue 586 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 299 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 232 optimal weight: 0.0070 chunk 43 optimal weight: 0.8980 chunk 369 optimal weight: 0.0470 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1171 ASN C 65 ASN C 207 HIS C 216 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.5135 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: