Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 07:15:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/10_2023/6rqt_4985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/10_2023/6rqt_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_4985/10_2023/6rqt_4985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/10_2023/6rqt_4985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/10_2023/6rqt_4985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqt_4985/10_2023/6rqt_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-1.21rc1-5097/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: 19.36, 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: 14.64 Conformation dependent library (CDL) restraints added in 5.4 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: 4.45 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: 16.45 Time building geometry restraints manager: 16.00 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: 23935 29.92 - 59.83: 690 59.83 - 89.75: 61 89.75 - 119.67: 0 119.67 - 149.58: 2 Dihedral angle restraints: 24688 sinusoidal: 10342 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 24685 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: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.940 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 103.770 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.330 ------------------------------------------------------------------------------- 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 : 13.820 149.581 15400 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 *********************** 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 : 4.450 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 outliers start: 59 outliers final: 11 residues processed: 1183 average time/residue: 0.5689 time to fit residues: 1057.2692 Evaluate side-chains 599 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 588 time to evaluate : 4.866 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3504 time to fit residues: 14.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.0870 chunk 369 optimal weight: 0.2980 chunk 205 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 232 optimal weight: 0.0980 chunk 284 optimal weight: 8.9990 chunk 443 optimal weight: 20.0000 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS A 224 HIS A 257 ASN A 336 GLN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 515 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1072 ASN A1088 HIS ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1437 ASN A1567 ASN ** 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 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 422 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 598 HIS B 711 GLN 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 HIS B1041 ASN B1045 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1157 GLN B1171 ASN C 323 ASN D 38 GLN E 146 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 104 ASN G 8 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 O 390 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40654 Z= 0.211 Angle : 0.754 11.864 55055 Z= 0.390 Chirality : 0.047 0.266 6173 Planarity : 0.006 0.117 6974 Dihedral : 11.009 153.892 5632 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.00 % Favored : 89.94 % Rotamer: Outliers : 3.50 % Allowed : 16.20 % Favored : 80.30 % 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: -4.70 (0.10), residues: 4839 helix: -3.87 (0.09), residues: 1268 sheet: -3.16 (0.20), residues: 517 loop : -2.91 (0.10), residues: 3054 *********************** 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 860 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 707 time to evaluate : 5.480 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 outliers start: 153 outliers final: 49 residues processed: 819 average time/residue: 0.4726 time to fit residues: 640.6651 Evaluate side-chains 613 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 564 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3043 time to fit residues: 32.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 443 optimal weight: 30.0000 chunk 479 optimal weight: 1.9990 chunk 395 optimal weight: 20.0000 chunk 440 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1036 ASN A1072 ASN ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1500 GLN ** 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 600 GLN B 686 HIS ** 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 B 999 GLN B1010 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1157 GLN C 65 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 20 HIS G 23 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 ASN ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 152 GLN O 411 ASN O 478 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 40654 Z= 0.329 Angle : 0.820 10.628 55055 Z= 0.425 Chirality : 0.050 0.278 6173 Planarity : 0.007 0.151 6974 Dihedral : 10.961 149.225 5632 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.66 % Favored : 86.30 % Rotamer: Outliers : 4.48 % Allowed : 18.62 % 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: -4.48 (0.11), residues: 4839 helix: -3.52 (0.10), residues: 1295 sheet: -3.05 (0.21), residues: 486 loop : -2.83 (0.11), residues: 3058 *********************** 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 815 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 619 time to evaluate : 4.991 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 outliers start: 196 outliers final: 91 residues processed: 759 average time/residue: 0.5095 time to fit residues: 644.3282 Evaluate side-chains 605 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 514 time to evaluate : 4.808 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 91 outliers final: 1 residues processed: 91 average time/residue: 0.3860 time to fit residues: 72.0846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 7.9990 chunk 333 optimal weight: 0.6980 chunk 230 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 298 optimal weight: 0.3980 chunk 445 optimal weight: 2.9990 chunk 471 optimal weight: 0.0040 chunk 232 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 477 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1500 GLN ** A1525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN A1647 ASN B 45 HIS B 171 HIS B 183 HIS B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** 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** B 999 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1114 GLN C 65 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 216 HIS E 153 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 140 GLN N 51 GLN N 52 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN O 390 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40654 Z= 0.168 Angle : 0.682 11.227 55055 Z= 0.347 Chirality : 0.045 0.235 6173 Planarity : 0.005 0.117 6974 Dihedral : 10.311 152.506 5632 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.05 % Favored : 90.91 % Rotamer: Outliers : 2.33 % Allowed : 20.66 % Favored : 77.01 % 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: -4.07 (0.11), residues: 4839 helix: -3.19 (0.11), residues: 1302 sheet: -2.65 (0.22), residues: 477 loop : -2.59 (0.11), residues: 3060 *********************** 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 711 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 609 time to evaluate : 4.697 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 outliers start: 102 outliers final: 36 residues processed: 681 average time/residue: 0.5143 time to fit residues: 585.8213 Evaluate side-chains 544 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 508 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3839 time to fit residues: 32.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 194 optimal weight: 0.0570 chunk 402 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 240 optimal weight: 0.5980 chunk 423 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 overall best weight: 4.1304 ------------------------------------------------------------------------------- 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 515 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 636 HIS A 640 ASN A 753 ASN A 998 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1503 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 168 ASN ** 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 473 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1094 ASN C 207 HIS ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40654 Z= 0.289 Angle : 0.750 9.501 55055 Z= 0.383 Chirality : 0.048 0.218 6173 Planarity : 0.006 0.133 6974 Dihedral : 10.451 149.677 5632 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.23 % Favored : 86.73 % Rotamer: Outliers : 3.22 % Allowed : 21.66 % 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: -4.04 (0.11), residues: 4839 helix: -3.11 (0.11), residues: 1320 sheet: -2.83 (0.21), residues: 515 loop : -2.54 (0.11), residues: 3004 *********************** 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 662 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 521 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 75 residues processed: 624 average time/residue: 0.5096 time to fit residues: 537.1864 Evaluate side-chains 558 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 483 time to evaluate : 4.665 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.3927 time to fit residues: 61.9715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.9980 chunk 424 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 391 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 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 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 207 HIS C 216 HIS C 248 GLN ** 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** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS O 117 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40654 Z= 0.230 Angle : 0.709 12.352 55055 Z= 0.359 Chirality : 0.046 0.212 6173 Planarity : 0.005 0.132 6974 Dihedral : 10.305 150.286 5632 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.89 % Favored : 89.07 % Rotamer: Outliers : 2.17 % Allowed : 22.78 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.11), residues: 4839 helix: -2.94 (0.12), residues: 1314 sheet: -2.71 (0.21), residues: 526 loop : -2.51 (0.11), residues: 2999 *********************** 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 649 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 554 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 49 residues processed: 618 average time/residue: 0.5324 time to fit residues: 551.2688 Evaluate side-chains 546 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 497 time to evaluate : 4.945 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4234 time to fit residues: 44.6747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 470 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 286 optimal weight: 0.1980 chunk 217 optimal weight: 7.9990 overall best weight: 2.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS ** A1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 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 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 248 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40654 Z= 0.209 Angle : 0.687 10.120 55055 Z= 0.349 Chirality : 0.045 0.203 6173 Planarity : 0.005 0.108 6974 Dihedral : 10.179 150.037 5632 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.03 % Favored : 87.93 % Rotamer: Outliers : 1.74 % Allowed : 23.74 % Favored : 74.52 % 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: -3.79 (0.11), residues: 4839 helix: -2.80 (0.12), residues: 1311 sheet: -2.58 (0.21), residues: 502 loop : -2.46 (0.11), residues: 3026 *********************** 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 601 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 525 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 43 residues processed: 574 average time/residue: 0.5200 time to fit residues: 498.9782 Evaluate side-chains 528 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 485 time to evaluate : 4.609 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3933 time to fit residues: 37.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS ** A1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 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 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 216 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 16 GLN M 54 HIS ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40654 Z= 0.225 Angle : 0.701 11.283 55055 Z= 0.354 Chirality : 0.046 0.332 6173 Planarity : 0.005 0.114 6974 Dihedral : 10.166 149.473 5632 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.63 % Favored : 88.32 % Rotamer: Outliers : 1.28 % Allowed : 24.27 % Favored : 74.45 % 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: -3.72 (0.11), residues: 4839 helix: -2.70 (0.12), residues: 1323 sheet: -2.55 (0.22), residues: 515 loop : -2.43 (0.11), residues: 3001 *********************** REFINEMENT MACRO_CYCLE 8 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 571 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 515 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 26 residues processed: 546 average time/residue: 0.5221 time to fit residues: 476.0975 Evaluate side-chains 506 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 480 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4080 time to fit residues: 26.0052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 0.6980 chunk 450 optimal weight: 1.9990 chunk 411 optimal weight: 8.9990 chunk 438 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 396 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 436 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1293 HIS A1299 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** 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 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 296 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** ** N 34 HIS ** 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: 0.6039 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40654 Z= 0.178 Angle : 0.671 10.178 55055 Z= 0.337 Chirality : 0.044 0.268 6173 Planarity : 0.005 0.092 6974 Dihedral : 9.975 150.128 5632 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.21 % Favored : 89.75 % Rotamer: Outliers : 0.75 % Allowed : 24.91 % Favored : 74.34 % 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: -3.53 (0.11), residues: 4839 helix: -2.50 (0.13), residues: 1314 sheet: -2.46 (0.21), residues: 535 loop : -2.33 (0.11), residues: 2990 *********************** REFINEMENT MACRO_CYCLE 9 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 561 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 528 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 551 average time/residue: 0.5292 time to fit residues: 490.7786 Evaluate side-chains 504 residues out of total 4381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 491 time to evaluate : 4.243 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3924 time to fit residues: 15.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 282 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 486 optimal weight: 0.1980 chunk 447 optimal weight: 7.9990 chunk 387 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 299 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: