Starting phenix.real_space_refine (version: dev) on Thu Dec 15 10:41:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eaq_27982/12_2022/8eaq_27982_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2002": "OE1" <-> "OE2" Residue "A TYR 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2425": "OE1" <-> "OE2" Residue "A PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2002": "OE1" <-> "OE2" Residue "B TYR 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2425": "OE1" <-> "OE2" Residue "B PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2002": "OE1" <-> "OE2" Residue "C TYR 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2425": "OE1" <-> "OE2" Residue "C PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 726": "OD1" <-> "OD2" Residue "D PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2002": "OE1" <-> "OE2" Residue "D TYR 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2425": "OE1" <-> "OE2" Residue "D PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 77928 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 19195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 Conformer: "B" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 bond proxies already assigned to first conformer: 19517 Chain: "B" Number of atoms: 19195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 Conformer: "B" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 bond proxies already assigned to first conformer: 19517 Chain: "C" Number of atoms: 19195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 Conformer: "B" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 bond proxies already assigned to first conformer: 19517 Chain: "D" Number of atoms: 19195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 Conformer: "B" Number of residues, atoms: 2374, 19184 Classifications: {'peptide': 2374} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 2301} Chain breaks: 11 bond proxies already assigned to first conformer: 19517 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Unusual residues: {' CA': 6, ' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 83 Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 287 Unusual residues: {' CA': 5, ' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 83 Chain: "C" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 287 Unusual residues: {' CA': 5, ' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 83 Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 286 Unusual residues: {' CA': 4, ' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 83 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18125 SG CYS A2611 134.803 147.500 113.146 1.00 37.52 S ATOM 18150 SG CYS A2614 132.382 146.309 110.733 1.00 46.22 S ATOM 37320 SG CYS B2611 147.576 121.998 113.193 1.00 37.52 S ATOM 37345 SG CYS B2614 146.382 124.416 110.779 1.00 46.22 S ATOM 56515 SG CYS C2611 109.221 134.799 113.192 1.00 37.52 S ATOM 56540 SG CYS C2614 110.416 132.381 110.777 1.00 46.22 S ATOM 75710 SG CYS D2611 122.003 109.225 113.195 1.00 37.52 S ATOM 75735 SG CYS D2614 124.421 110.420 110.781 1.00 46.22 S Time building chain proxies: 57.00, per 1000 atoms: 0.73 Number of scatterers: 77928 At special positions: 0 Unit cell: (257.87, 257.87, 200.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 20 19.99 S 472 16.00 P 28 15.00 O 14492 8.00 N 13312 7.00 C 49600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2528 " - pdb=" SG CYS A2534 " distance=2.04 Simple disulfide: pdb=" SG CYS B2528 " - pdb=" SG CYS B2534 " distance=2.04 Simple disulfide: pdb=" SG CYS C2528 " - pdb=" SG CYS C2534 " distance=2.04 Simple disulfide: pdb=" SG CYS D2528 " - pdb=" SG CYS D2534 " distance=2.04 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.02 Conformation dependent library (CDL) restraints added in 16.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A2631 " pdb="ZN ZN A5101 " - pdb=" ND1 HIS A2636 " pdb="ZN ZN A5101 " - pdb=" SG CYS A2614 " pdb="ZN ZN A5101 " - pdb=" SG CYS A2611 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B2631 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B2636 " pdb="ZN ZN B5101 " - pdb=" SG CYS B2614 " pdb="ZN ZN B5101 " - pdb=" SG CYS B2611 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C2631 " pdb="ZN ZN C5101 " - pdb=" ND1 HIS C2636 " pdb="ZN ZN C5101 " - pdb=" SG CYS C2614 " pdb="ZN ZN C5101 " - pdb=" SG CYS C2611 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D2631 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D2636 " pdb="ZN ZN D5101 " - pdb=" SG CYS D2614 " pdb="ZN ZN D5101 " - pdb=" SG CYS D2611 " Number of angles added : 4 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 428 helices and 60 sheets defined 59.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.77 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.987A pdb=" N GLU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 462 removed outlier: 4.069A pdb=" N LYS A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 485 Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.945A pdb=" N GLY A 542 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 564 Proline residue: A 548 - end of helix Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.729A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 600 Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 612 through 624 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 646 through 656 Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'A' and resid 724 through 743 Processing helix chain 'A' and resid 749 through 755 removed outlier: 5.292A pdb=" N GLU A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 826 through 849 removed outlier: 5.046A pdb=" N ARG A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 removed outlier: 4.093A pdb=" N LYS A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 Processing helix chain 'A' and resid 965 through 1007 removed outlier: 3.539A pdb=" N ILE A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 977 " --> pdb=" O LYS A 973 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A1003 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A1006 " --> pdb=" O ASP A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1039 removed outlier: 3.512A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1073 through 1087 Processing helix chain 'A' and resid 1089 through 1098 Processing helix chain 'A' and resid 1107 through 1127 removed outlier: 3.660A pdb=" N TYR A1112 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A1117 " --> pdb=" O GLN A1114 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A1118 " --> pdb=" O ILE A1115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A1119 " --> pdb=" O LYS A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1132 No H-bonds generated for 'chain 'A' and resid 1129 through 1132' Processing helix chain 'A' and resid 1168 through 1186 Processing helix chain 'A' and resid 1199 through 1208 Processing helix chain 'A' and resid 1211 through 1218 removed outlier: 4.692A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1244 Processing helix chain 'A' and resid 1249 through 1261 removed outlier: 4.115A pdb=" N LYS A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN A1260 " --> pdb=" O HIS A1256 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A1261 " --> pdb=" O LYS A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 Processing helix chain 'A' and resid 1281 through 1286 Processing helix chain 'A' and resid 1289 through 1302 Processing helix chain 'A' and resid 1306 through 1316 Processing helix chain 'A' and resid 1324 through 1340 removed outlier: 5.999A pdb=" N GLU A1339 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.651A pdb=" N THR A1353 " --> pdb=" O ALA A1349 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A1359 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1386 Processing helix chain 'A' and resid 1391 through 1400 removed outlier: 3.630A pdb=" N LYS A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1411 Processing helix chain 'A' and resid 1417 through 1431 removed outlier: 4.288A pdb=" N ALA A1422 " --> pdb=" O GLU A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1446 through 1466 removed outlier: 4.237A pdb=" N SER A1466 " --> pdb=" O CYS A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1492 removed outlier: 3.777A pdb=" N VAL A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET A1484 " --> pdb=" O THR A1480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A1487 " --> pdb=" O VAL A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1498 removed outlier: 3.780A pdb=" N GLN A1498 " --> pdb=" O PRO A1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1494 through 1498' Processing helix chain 'A' and resid 1500 through 1504 removed outlier: 3.807A pdb=" N THR A1504 " --> pdb=" O THR A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1527 through 1547 Processing helix chain 'A' and resid 1553 through 1563 Processing helix chain 'A' and resid 1589 through 1631 Proline residue: A1617 - end of helix Processing helix chain 'A' and resid 1633 through 1636 removed outlier: 3.525A pdb=" N LEU A1636 " --> pdb=" O PRO A1633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1633 through 1636' Processing helix chain 'A' and resid 1642 through 1649 removed outlier: 3.765A pdb=" N SER A1649 " --> pdb=" O ARG A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1661 Processing helix chain 'A' and resid 1663 through 1666 removed outlier: 3.591A pdb=" N GLU A1666 " --> pdb=" O LEU A1663 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1663 through 1666' Processing helix chain 'A' and resid 1669 through 1683 removed outlier: 4.164A pdb=" N MET A1683 " --> pdb=" O LEU A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1745 Processing helix chain 'A' and resid 1792 through 1802 removed outlier: 3.633A pdb=" N GLU A1802 " --> pdb=" O HIS A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1813 Processing helix chain 'A' and resid 1818 through 1832 Processing helix chain 'A' and resid 1837 through 1849 Processing helix chain 'A' and resid 1853 through 1874 removed outlier: 3.775A pdb=" N PHE A1860 " --> pdb=" O PHE A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1980 removed outlier: 4.395A pdb=" N MET A1966 " --> pdb=" O VAL A1962 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN A1967 " --> pdb=" O ILE A1963 " (cutoff:3.500A) Proline residue: A1968 - end of helix removed outlier: 3.996A pdb=" N CYS A1977 " --> pdb=" O LEU A1973 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN A1979 " --> pdb=" O LEU A1975 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N HIS A1980 " --> pdb=" O LEU A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1987 Processing helix chain 'A' and resid 1999 through 2011 Processing helix chain 'A' and resid 2013 through 2018 removed outlier: 3.820A pdb=" N GLY A2017 " --> pdb=" O SER A2013 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A2018 " --> pdb=" O THR A2014 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2013 through 2018' Processing helix chain 'A' and resid 2030 through 2044 Processing helix chain 'A' and resid 2049 through 2056 Processing helix chain 'A' and resid 2062 through 2071 Processing helix chain 'A' and resid 2077 through 2080 No H-bonds generated for 'chain 'A' and resid 2077 through 2080' Processing helix chain 'A' and resid 2082 through 2099 Processing helix chain 'A' and resid 2109 through 2115 Processing helix chain 'A' and resid 2118 through 2138 removed outlier: 3.561A pdb=" N TYR A2129 " --> pdb=" O ILE A2125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A2130 " --> pdb=" O LYS A2126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A2138 " --> pdb=" O VAL A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2166 removed outlier: 4.235A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HIS A2166 " --> pdb=" O GLN A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2174 Processing helix chain 'A' and resid 2183 through 2190 Processing helix chain 'A' and resid 2214 through 2217 removed outlier: 3.561A pdb=" N GLU A2217 " --> pdb=" O SER A2214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2214 through 2217' Processing helix chain 'A' and resid 2221 through 2230 Processing helix chain 'A' and resid 2240 through 2262 removed outlier: 3.538A pdb=" N ARG A2246 " --> pdb=" O ASP A2242 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A2247 " --> pdb=" O PHE A2243 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU A2248 " --> pdb=" O PHE A2244 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP A2249 " --> pdb=" O LEU A2245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A2261 " --> pdb=" O GLN A2257 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A2262 " --> pdb=" O LYS A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2270 removed outlier: 3.576A pdb=" N TRP A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2273 through 2293 Processing helix chain 'A' and resid 2329 through 2347 Processing helix chain 'A' and resid 2351 through 2376 Processing helix chain 'A' and resid 2378 through 2381 Processing helix chain 'A' and resid 2383 through 2388 Processing helix chain 'A' and resid 2391 through 2407 Processing helix chain 'A' and resid 2410 through 2423 Processing helix chain 'A' and resid 2425 through 2435 removed outlier: 4.038A pdb=" N VAL A2434 " --> pdb=" O VAL A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2462 Processing helix chain 'A' and resid 2464 through 2466 No H-bonds generated for 'chain 'A' and resid 2464 through 2466' Processing helix chain 'A' and resid 2531 through 2541 Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2563 through 2577 Processing helix chain 'A' and resid 2581 through 2608 removed outlier: 3.896A pdb=" N ARG A2597 " --> pdb=" O PHE A2593 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2621 Processing helix chain 'A' and resid 2628 through 2634 removed outlier: 3.665A pdb=" N LYS A2633 " --> pdb=" O GLU A2629 " (cutoff:3.500A) Processing helix chain 'A' and resid 2638 through 2650 Processing helix chain 'A' and resid 2653 through 2655 No H-bonds generated for 'chain 'A' and resid 2653 through 2655' Processing helix chain 'A' and resid 2658 through 2668 Processing helix chain 'A' and resid 2689 through 2736 removed outlier: 3.541A pdb=" N THR A2710 " --> pdb=" O LYS A2707 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A2736 " --> pdb=" O ILE A2733 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 86 through 109 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.987A pdb=" N GLU B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 462 removed outlier: 4.069A pdb=" N LYS B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 485 Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.945A pdb=" N GLY B 542 " --> pdb=" O GLU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 564 Proline residue: B 548 - end of helix Processing helix chain 'B' and resid 568 through 582 removed outlier: 3.729A pdb=" N LYS B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 612 through 624 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 646 through 656 Processing helix chain 'B' and resid 658 through 661 No H-bonds generated for 'chain 'B' and resid 658 through 661' Processing helix chain 'B' and resid 712 through 721 Processing helix chain 'B' and resid 724 through 743 Processing helix chain 'B' and resid 749 through 755 removed outlier: 5.291A pdb=" N GLU B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 Processing helix chain 'B' and resid 775 through 789 Processing helix chain 'B' and resid 826 through 849 removed outlier: 5.047A pdb=" N ARG B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 833 " --> pdb=" O ILE B 829 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR B 836 " --> pdb=" O ARG B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 875 removed outlier: 4.093A pdb=" N LYS B 861 " --> pdb=" O LYS B 857 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 862 " --> pdb=" O GLU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 901 Processing helix chain 'B' and resid 965 through 1007 removed outlier: 3.540A pdb=" N ILE B 974 " --> pdb=" O THR B 970 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 975 " --> pdb=" O LYS B 971 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B1003 " --> pdb=" O ARG B 999 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1004 " --> pdb=" O GLU B1000 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B1006 " --> pdb=" O ASP B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1039 removed outlier: 3.512A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 Processing helix chain 'B' and resid 1073 through 1087 Processing helix chain 'B' and resid 1089 through 1098 Processing helix chain 'B' and resid 1107 through 1127 removed outlier: 3.660A pdb=" N TYR B1112 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B1117 " --> pdb=" O GLN B1114 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B1118 " --> pdb=" O ILE B1115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B1119 " --> pdb=" O LYS B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1132 No H-bonds generated for 'chain 'B' and resid 1129 through 1132' Processing helix chain 'B' and resid 1168 through 1186 Processing helix chain 'B' and resid 1199 through 1208 Processing helix chain 'B' and resid 1211 through 1218 removed outlier: 4.692A pdb=" N GLU B1216 " --> pdb=" O ALA B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1244 Processing helix chain 'B' and resid 1249 through 1261 removed outlier: 4.115A pdb=" N LYS B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS B1258 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASN B1260 " --> pdb=" O HIS B1256 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B1261 " --> pdb=" O LYS B1257 " (cutoff:3.500A) Processing helix chain 'B' and resid 1267 through 1277 Processing helix chain 'B' and resid 1281 through 1286 Processing helix chain 'B' and resid 1289 through 1302 Processing helix chain 'B' and resid 1306 through 1316 Processing helix chain 'B' and resid 1324 through 1340 removed outlier: 6.000A pdb=" N GLU B1339 " --> pdb=" O VAL B1335 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP B1340 " --> pdb=" O ASN B1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1361 removed outlier: 3.651A pdb=" N THR B1353 " --> pdb=" O ALA B1349 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B1359 " --> pdb=" O ILE B1355 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B1360 " --> pdb=" O GLN B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1386 Processing helix chain 'B' and resid 1391 through 1400 removed outlier: 3.630A pdb=" N LYS B1396 " --> pdb=" O TYR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1417 through 1431 removed outlier: 4.289A pdb=" N ALA B1422 " --> pdb=" O GLU B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1442 Processing helix chain 'B' and resid 1446 through 1466 removed outlier: 4.237A pdb=" N SER B1466 " --> pdb=" O CYS B1462 " (cutoff:3.500A) Processing helix chain 'B' and resid 1473 through 1492 removed outlier: 3.777A pdb=" N VAL B1483 " --> pdb=" O VAL B1479 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET B1484 " --> pdb=" O THR B1480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1487 " --> pdb=" O VAL B1483 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1498 removed outlier: 3.780A pdb=" N GLN B1498 " --> pdb=" O PRO B1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1494 through 1498' Processing helix chain 'B' and resid 1500 through 1504 removed outlier: 3.806A pdb=" N THR B1504 " --> pdb=" O THR B1501 " (cutoff:3.500A) Processing helix chain 'B' and resid 1506 through 1520 Processing helix chain 'B' and resid 1527 through 1547 Processing helix chain 'B' and resid 1553 through 1563 Processing helix chain 'B' and resid 1589 through 1631 Proline residue: B1617 - end of helix Processing helix chain 'B' and resid 1633 through 1636 removed outlier: 3.525A pdb=" N LEU B1636 " --> pdb=" O PRO B1633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1633 through 1636' Processing helix chain 'B' and resid 1642 through 1649 removed outlier: 3.764A pdb=" N SER B1649 " --> pdb=" O ARG B1645 " (cutoff:3.500A) Processing helix chain 'B' and resid 1651 through 1661 Processing helix chain 'B' and resid 1663 through 1666 removed outlier: 3.591A pdb=" N GLU B1666 " --> pdb=" O LEU B1663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1663 through 1666' Processing helix chain 'B' and resid 1669 through 1683 removed outlier: 4.165A pdb=" N MET B1683 " --> pdb=" O LEU B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1722 through 1745 Processing helix chain 'B' and resid 1792 through 1802 removed outlier: 3.632A pdb=" N GLU B1802 " --> pdb=" O HIS B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1813 Processing helix chain 'B' and resid 1818 through 1832 Processing helix chain 'B' and resid 1837 through 1849 Processing helix chain 'B' and resid 1853 through 1874 removed outlier: 3.775A pdb=" N PHE B1860 " --> pdb=" O PHE B1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 1961 through 1980 removed outlier: 4.395A pdb=" N MET B1966 " --> pdb=" O VAL B1962 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B1967 " --> pdb=" O ILE B1963 " (cutoff:3.500A) Proline residue: B1968 - end of helix removed outlier: 3.996A pdb=" N CYS B1977 " --> pdb=" O LEU B1973 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN B1979 " --> pdb=" O LEU B1975 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N HIS B1980 " --> pdb=" O LEU B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1982 through 1987 Processing helix chain 'B' and resid 1999 through 2011 Processing helix chain 'B' and resid 2013 through 2018 removed outlier: 3.821A pdb=" N GLY B2017 " --> pdb=" O SER B2013 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B2018 " --> pdb=" O THR B2014 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2013 through 2018' Processing helix chain 'B' and resid 2030 through 2044 Processing helix chain 'B' and resid 2049 through 2056 Processing helix chain 'B' and resid 2062 through 2071 Processing helix chain 'B' and resid 2077 through 2080 No H-bonds generated for 'chain 'B' and resid 2077 through 2080' Processing helix chain 'B' and resid 2082 through 2099 Processing helix chain 'B' and resid 2109 through 2115 Processing helix chain 'B' and resid 2118 through 2138 removed outlier: 3.561A pdb=" N TYR B2129 " --> pdb=" O ILE B2125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B2130 " --> pdb=" O LYS B2126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B2138 " --> pdb=" O VAL B2134 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2166 removed outlier: 4.235A pdb=" N ARG B2165 " --> pdb=" O HIS B2161 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N HIS B2166 " --> pdb=" O GLN B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2174 Processing helix chain 'B' and resid 2183 through 2190 Processing helix chain 'B' and resid 2214 through 2217 removed outlier: 3.560A pdb=" N GLU B2217 " --> pdb=" O SER B2214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2214 through 2217' Processing helix chain 'B' and resid 2221 through 2230 Processing helix chain 'B' and resid 2240 through 2262 removed outlier: 3.538A pdb=" N ARG B2246 " --> pdb=" O ASP B2242 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B2247 " --> pdb=" O PHE B2243 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU B2248 " --> pdb=" O PHE B2244 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP B2249 " --> pdb=" O LEU B2245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B2261 " --> pdb=" O GLN B2257 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA B2262 " --> pdb=" O LYS B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2264 through 2270 removed outlier: 3.577A pdb=" N TRP B2268 " --> pdb=" O PRO B2264 " (cutoff:3.500A) Processing helix chain 'B' and resid 2273 through 2293 Processing helix chain 'B' and resid 2329 through 2347 Processing helix chain 'B' and resid 2351 through 2376 Processing helix chain 'B' and resid 2378 through 2381 Processing helix chain 'B' and resid 2383 through 2388 Processing helix chain 'B' and resid 2391 through 2407 Processing helix chain 'B' and resid 2410 through 2423 Processing helix chain 'B' and resid 2425 through 2435 removed outlier: 4.038A pdb=" N VAL B2434 " --> pdb=" O VAL B2430 " (cutoff:3.500A) Processing helix chain 'B' and resid 2438 through 2462 Processing helix chain 'B' and resid 2464 through 2466 No H-bonds generated for 'chain 'B' and resid 2464 through 2466' Processing helix chain 'B' and resid 2531 through 2541 Processing helix chain 'B' and resid 2549 through 2551 No H-bonds generated for 'chain 'B' and resid 2549 through 2551' Processing helix chain 'B' and resid 2563 through 2577 Processing helix chain 'B' and resid 2581 through 2608 removed outlier: 3.895A pdb=" N ARG B2597 " --> pdb=" O PHE B2593 " (cutoff:3.500A) Processing helix chain 'B' and resid 2618 through 2621 Processing helix chain 'B' and resid 2628 through 2634 removed outlier: 3.664A pdb=" N LYS B2633 " --> pdb=" O GLU B2629 " (cutoff:3.500A) Processing helix chain 'B' and resid 2638 through 2650 Processing helix chain 'B' and resid 2653 through 2655 No H-bonds generated for 'chain 'B' and resid 2653 through 2655' Processing helix chain 'B' and resid 2658 through 2668 Processing helix chain 'B' and resid 2689 through 2736 removed outlier: 3.541A pdb=" N THR B2710 " --> pdb=" O LYS B2707 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B2736 " --> pdb=" O ILE B2733 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 86 through 109 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.987A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 462 removed outlier: 4.069A pdb=" N LYS C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 485 Processing helix chain 'C' and resid 504 through 512 Processing helix chain 'C' and resid 515 through 525 Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.946A pdb=" N GLY C 542 " --> pdb=" O GLU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 564 Proline residue: C 548 - end of helix Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.730A pdb=" N LYS C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE C 580 " --> pdb=" O LYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 600 Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 612 through 624 Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 646 through 656 Processing helix chain 'C' and resid 658 through 661 No H-bonds generated for 'chain 'C' and resid 658 through 661' Processing helix chain 'C' and resid 712 through 721 Processing helix chain 'C' and resid 724 through 743 Processing helix chain 'C' and resid 749 through 755 removed outlier: 5.292A pdb=" N GLU C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 769 Processing helix chain 'C' and resid 775 through 789 Processing helix chain 'C' and resid 826 through 849 removed outlier: 5.046A pdb=" N ARG C 832 " --> pdb=" O GLU C 828 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 833 " --> pdb=" O ILE C 829 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN C 835 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR C 836 " --> pdb=" O ARG C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 875 removed outlier: 4.093A pdb=" N LYS C 861 " --> pdb=" O LYS C 857 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 862 " --> pdb=" O GLU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 901 Processing helix chain 'C' and resid 965 through 1007 removed outlier: 3.539A pdb=" N ILE C 974 " --> pdb=" O THR C 970 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 975 " --> pdb=" O LYS C 971 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 977 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C1003 " --> pdb=" O ARG C 999 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C1004 " --> pdb=" O GLU C1000 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C1006 " --> pdb=" O ASP C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1039 removed outlier: 3.512A pdb=" N GLY C1039 " --> pdb=" O GLU C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1066 Processing helix chain 'C' and resid 1073 through 1087 Processing helix chain 'C' and resid 1089 through 1098 Processing helix chain 'C' and resid 1107 through 1127 removed outlier: 3.660A pdb=" N TYR C1112 " --> pdb=" O VAL C1109 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN C1117 " --> pdb=" O GLN C1114 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C1118 " --> pdb=" O ILE C1115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C1119 " --> pdb=" O LYS C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1132 No H-bonds generated for 'chain 'C' and resid 1129 through 1132' Processing helix chain 'C' and resid 1168 through 1186 Processing helix chain 'C' and resid 1199 through 1208 Processing helix chain 'C' and resid 1211 through 1218 removed outlier: 4.692A pdb=" N GLU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1229 through 1244 Processing helix chain 'C' and resid 1249 through 1261 removed outlier: 4.116A pdb=" N LYS C1257 " --> pdb=" O ALA C1253 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS C1258 " --> pdb=" O LEU C1254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C1259 " --> pdb=" O LEU C1255 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN C1260 " --> pdb=" O HIS C1256 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C1261 " --> pdb=" O LYS C1257 " (cutoff:3.500A) Processing helix chain 'C' and resid 1267 through 1277 Processing helix chain 'C' and resid 1281 through 1286 Processing helix chain 'C' and resid 1289 through 1302 Processing helix chain 'C' and resid 1306 through 1316 Processing helix chain 'C' and resid 1324 through 1340 removed outlier: 5.998A pdb=" N GLU C1339 " --> pdb=" O VAL C1335 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP C1340 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1361 removed outlier: 3.651A pdb=" N THR C1353 " --> pdb=" O ALA C1349 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C1359 " --> pdb=" O ILE C1355 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C1360 " --> pdb=" O GLN C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1372 through 1386 Processing helix chain 'C' and resid 1391 through 1400 removed outlier: 3.630A pdb=" N LYS C1396 " --> pdb=" O TYR C1392 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1411 Processing helix chain 'C' and resid 1417 through 1431 removed outlier: 4.289A pdb=" N ALA C1422 " --> pdb=" O GLU C1418 " (cutoff:3.500A) Processing helix chain 'C' and resid 1439 through 1442 Processing helix chain 'C' and resid 1446 through 1466 removed outlier: 4.238A pdb=" N SER C1466 " --> pdb=" O CYS C1462 " (cutoff:3.500A) Processing helix chain 'C' and resid 1473 through 1492 removed outlier: 3.777A pdb=" N VAL C1483 " --> pdb=" O VAL C1479 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET C1484 " --> pdb=" O THR C1480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C1487 " --> pdb=" O VAL C1483 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1498 removed outlier: 3.781A pdb=" N GLN C1498 " --> pdb=" O PRO C1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1494 through 1498' Processing helix chain 'C' and resid 1500 through 1504 removed outlier: 3.806A pdb=" N THR C1504 " --> pdb=" O THR C1501 " (cutoff:3.500A) Processing helix chain 'C' and resid 1506 through 1520 Processing helix chain 'C' and resid 1527 through 1547 Processing helix chain 'C' and resid 1553 through 1563 Processing helix chain 'C' and resid 1589 through 1631 Proline residue: C1617 - end of helix Processing helix chain 'C' and resid 1633 through 1636 removed outlier: 3.525A pdb=" N LEU C1636 " --> pdb=" O PRO C1633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1633 through 1636' Processing helix chain 'C' and resid 1642 through 1649 removed outlier: 3.765A pdb=" N SER C1649 " --> pdb=" O ARG C1645 " (cutoff:3.500A) Processing helix chain 'C' and resid 1651 through 1661 Processing helix chain 'C' and resid 1663 through 1666 removed outlier: 3.591A pdb=" N GLU C1666 " --> pdb=" O LEU C1663 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1663 through 1666' Processing helix chain 'C' and resid 1669 through 1683 removed outlier: 4.165A pdb=" N MET C1683 " --> pdb=" O LEU C1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 1722 through 1745 Processing helix chain 'C' and resid 1792 through 1802 removed outlier: 3.632A pdb=" N GLU C1802 " --> pdb=" O HIS C1798 " (cutoff:3.500A) Processing helix chain 'C' and resid 1804 through 1813 Processing helix chain 'C' and resid 1818 through 1832 Processing helix chain 'C' and resid 1837 through 1849 Processing helix chain 'C' and resid 1853 through 1874 removed outlier: 3.775A pdb=" N PHE C1860 " --> pdb=" O PHE C1856 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1980 removed outlier: 4.396A pdb=" N MET C1966 " --> pdb=" O VAL C1962 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN C1967 " --> pdb=" O ILE C1963 " (cutoff:3.500A) Proline residue: C1968 - end of helix removed outlier: 3.996A pdb=" N CYS C1977 " --> pdb=" O LEU C1973 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C1979 " --> pdb=" O LEU C1975 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N HIS C1980 " --> pdb=" O LEU C1976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1982 through 1987 Processing helix chain 'C' and resid 1999 through 2011 Processing helix chain 'C' and resid 2013 through 2018 removed outlier: 3.821A pdb=" N GLY C2017 " --> pdb=" O SER C2013 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C2018 " --> pdb=" O THR C2014 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2013 through 2018' Processing helix chain 'C' and resid 2030 through 2044 Processing helix chain 'C' and resid 2049 through 2056 Processing helix chain 'C' and resid 2062 through 2071 Processing helix chain 'C' and resid 2077 through 2080 No H-bonds generated for 'chain 'C' and resid 2077 through 2080' Processing helix chain 'C' and resid 2082 through 2099 Processing helix chain 'C' and resid 2109 through 2115 Processing helix chain 'C' and resid 2118 through 2138 removed outlier: 3.561A pdb=" N TYR C2129 " --> pdb=" O ILE C2125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET C2130 " --> pdb=" O LYS C2126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C2138 " --> pdb=" O VAL C2134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2166 removed outlier: 4.235A pdb=" N ARG C2165 " --> pdb=" O HIS C2161 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HIS C2166 " --> pdb=" O GLN C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2168 through 2174 Processing helix chain 'C' and resid 2183 through 2190 Processing helix chain 'C' and resid 2214 through 2217 removed outlier: 3.561A pdb=" N GLU C2217 " --> pdb=" O SER C2214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2214 through 2217' Processing helix chain 'C' and resid 2221 through 2230 Processing helix chain 'C' and resid 2240 through 2262 removed outlier: 3.538A pdb=" N ARG C2246 " --> pdb=" O ASP C2242 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C2247 " --> pdb=" O PHE C2243 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU C2248 " --> pdb=" O PHE C2244 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP C2249 " --> pdb=" O LEU C2245 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C2261 " --> pdb=" O GLN C2257 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA C2262 " --> pdb=" O LYS C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2264 through 2270 removed outlier: 3.576A pdb=" N TRP C2268 " --> pdb=" O PRO C2264 " (cutoff:3.500A) Processing helix chain 'C' and resid 2273 through 2293 Processing helix chain 'C' and resid 2329 through 2347 Processing helix chain 'C' and resid 2351 through 2376 Processing helix chain 'C' and resid 2378 through 2381 Processing helix chain 'C' and resid 2383 through 2388 Processing helix chain 'C' and resid 2391 through 2407 Processing helix chain 'C' and resid 2410 through 2423 Processing helix chain 'C' and resid 2425 through 2435 removed outlier: 4.038A pdb=" N VAL C2434 " --> pdb=" O VAL C2430 " (cutoff:3.500A) Processing helix chain 'C' and resid 2438 through 2462 Processing helix chain 'C' and resid 2464 through 2466 No H-bonds generated for 'chain 'C' and resid 2464 through 2466' Processing helix chain 'C' and resid 2531 through 2541 Processing helix chain 'C' and resid 2549 through 2551 No H-bonds generated for 'chain 'C' and resid 2549 through 2551' Processing helix chain 'C' and resid 2563 through 2577 Processing helix chain 'C' and resid 2581 through 2608 removed outlier: 3.896A pdb=" N ARG C2597 " --> pdb=" O PHE C2593 " (cutoff:3.500A) Processing helix chain 'C' and resid 2618 through 2621 Processing helix chain 'C' and resid 2628 through 2634 removed outlier: 3.664A pdb=" N LYS C2633 " --> pdb=" O GLU C2629 " (cutoff:3.500A) Processing helix chain 'C' and resid 2638 through 2650 Processing helix chain 'C' and resid 2653 through 2655 No H-bonds generated for 'chain 'C' and resid 2653 through 2655' Processing helix chain 'C' and resid 2658 through 2668 Processing helix chain 'C' and resid 2689 through 2736 removed outlier: 3.541A pdb=" N THR C2710 " --> pdb=" O LYS C2707 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C2736 " --> pdb=" O ILE C2733 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 67 through 74 Processing helix chain 'D' and resid 86 through 109 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.986A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 462 removed outlier: 4.069A pdb=" N LYS D 462 " --> pdb=" O GLY D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 485 Processing helix chain 'D' and resid 504 through 512 Processing helix chain 'D' and resid 515 through 525 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.944A pdb=" N GLY D 542 " --> pdb=" O GLU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 564 Proline residue: D 548 - end of helix Processing helix chain 'D' and resid 568 through 582 removed outlier: 3.730A pdb=" N LYS D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 600 Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 612 through 624 Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 646 through 656 Processing helix chain 'D' and resid 658 through 661 No H-bonds generated for 'chain 'D' and resid 658 through 661' Processing helix chain 'D' and resid 712 through 721 Processing helix chain 'D' and resid 724 through 743 Processing helix chain 'D' and resid 749 through 755 removed outlier: 5.291A pdb=" N GLU D 754 " --> pdb=" O LEU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 769 Processing helix chain 'D' and resid 775 through 789 Processing helix chain 'D' and resid 826 through 849 removed outlier: 5.047A pdb=" N ARG D 832 " --> pdb=" O GLU D 828 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN D 835 " --> pdb=" O GLU D 831 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR D 836 " --> pdb=" O ARG D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 875 removed outlier: 4.093A pdb=" N LYS D 861 " --> pdb=" O LYS D 857 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D 862 " --> pdb=" O GLU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 901 Processing helix chain 'D' and resid 965 through 1007 removed outlier: 3.539A pdb=" N ILE D 974 " --> pdb=" O THR D 970 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 975 " --> pdb=" O LYS D 971 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 977 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D1003 " --> pdb=" O ARG D 999 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D1004 " --> pdb=" O GLU D1000 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D1006 " --> pdb=" O ASP D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1039 removed outlier: 3.512A pdb=" N GLY D1039 " --> pdb=" O GLU D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1066 Processing helix chain 'D' and resid 1073 through 1087 Processing helix chain 'D' and resid 1089 through 1098 Processing helix chain 'D' and resid 1107 through 1127 removed outlier: 3.660A pdb=" N TYR D1112 " --> pdb=" O VAL D1109 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN D1117 " --> pdb=" O GLN D1114 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D1118 " --> pdb=" O ILE D1115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D1119 " --> pdb=" O LYS D1116 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1132 No H-bonds generated for 'chain 'D' and resid 1129 through 1132' Processing helix chain 'D' and resid 1168 through 1186 Processing helix chain 'D' and resid 1199 through 1208 Processing helix chain 'D' and resid 1211 through 1218 removed outlier: 4.691A pdb=" N GLU D1216 " --> pdb=" O ALA D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1244 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.115A pdb=" N LYS D1257 " --> pdb=" O ALA D1253 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASN D1260 " --> pdb=" O HIS D1256 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D1261 " --> pdb=" O LYS D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1267 through 1277 Processing helix chain 'D' and resid 1281 through 1286 Processing helix chain 'D' and resid 1289 through 1302 Processing helix chain 'D' and resid 1306 through 1316 Processing helix chain 'D' and resid 1324 through 1340 removed outlier: 5.999A pdb=" N GLU D1339 " --> pdb=" O VAL D1335 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D1340 " --> pdb=" O ASN D1336 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1361 removed outlier: 3.650A pdb=" N THR D1353 " --> pdb=" O ALA D1349 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D1359 " --> pdb=" O ILE D1355 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D1360 " --> pdb=" O GLN D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1372 through 1386 Processing helix chain 'D' and resid 1391 through 1400 removed outlier: 3.630A pdb=" N LYS D1396 " --> pdb=" O TYR D1392 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1411 Processing helix chain 'D' and resid 1417 through 1431 removed outlier: 4.289A pdb=" N ALA D1422 " --> pdb=" O GLU D1418 " (cutoff:3.500A) Processing helix chain 'D' and resid 1439 through 1442 Processing helix chain 'D' and resid 1446 through 1466 removed outlier: 4.238A pdb=" N SER D1466 " --> pdb=" O CYS D1462 " (cutoff:3.500A) Processing helix chain 'D' and resid 1473 through 1492 removed outlier: 3.776A pdb=" N VAL D1483 " --> pdb=" O VAL D1479 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET D1484 " --> pdb=" O THR D1480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D1487 " --> pdb=" O VAL D1483 " (cutoff:3.500A) Processing helix chain 'D' and resid 1494 through 1498 removed outlier: 3.780A pdb=" N GLN D1498 " --> pdb=" O PRO D1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1494 through 1498' Processing helix chain 'D' and resid 1500 through 1504 removed outlier: 3.807A pdb=" N THR D1504 " --> pdb=" O THR D1501 " (cutoff:3.500A) Processing helix chain 'D' and resid 1506 through 1520 Processing helix chain 'D' and resid 1527 through 1547 Processing helix chain 'D' and resid 1553 through 1563 Processing helix chain 'D' and resid 1589 through 1631 Proline residue: D1617 - end of helix Processing helix chain 'D' and resid 1633 through 1636 removed outlier: 3.525A pdb=" N LEU D1636 " --> pdb=" O PRO D1633 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1633 through 1636' Processing helix chain 'D' and resid 1642 through 1649 removed outlier: 3.764A pdb=" N SER D1649 " --> pdb=" O ARG D1645 " (cutoff:3.500A) Processing helix chain 'D' and resid 1651 through 1661 Processing helix chain 'D' and resid 1663 through 1666 removed outlier: 3.591A pdb=" N GLU D1666 " --> pdb=" O LEU D1663 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1663 through 1666' Processing helix chain 'D' and resid 1669 through 1683 removed outlier: 4.164A pdb=" N MET D1683 " --> pdb=" O LEU D1679 " (cutoff:3.500A) Processing helix chain 'D' and resid 1722 through 1745 Processing helix chain 'D' and resid 1792 through 1802 removed outlier: 3.633A pdb=" N GLU D1802 " --> pdb=" O HIS D1798 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1813 Processing helix chain 'D' and resid 1818 through 1832 Processing helix chain 'D' and resid 1837 through 1849 Processing helix chain 'D' and resid 1853 through 1874 removed outlier: 3.775A pdb=" N PHE D1860 " --> pdb=" O PHE D1856 " (cutoff:3.500A) Processing helix chain 'D' and resid 1961 through 1980 removed outlier: 4.395A pdb=" N MET D1966 " --> pdb=" O VAL D1962 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN D1967 " --> pdb=" O ILE D1963 " (cutoff:3.500A) Proline residue: D1968 - end of helix removed outlier: 3.996A pdb=" N CYS D1977 " --> pdb=" O LEU D1973 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN D1979 " --> pdb=" O LEU D1975 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N HIS D1980 " --> pdb=" O LEU D1976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1982 through 1987 Processing helix chain 'D' and resid 1999 through 2011 Processing helix chain 'D' and resid 2013 through 2018 removed outlier: 3.821A pdb=" N GLY D2017 " --> pdb=" O SER D2013 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU D2018 " --> pdb=" O THR D2014 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2013 through 2018' Processing helix chain 'D' and resid 2030 through 2044 Processing helix chain 'D' and resid 2049 through 2056 Processing helix chain 'D' and resid 2062 through 2071 Processing helix chain 'D' and resid 2077 through 2080 No H-bonds generated for 'chain 'D' and resid 2077 through 2080' Processing helix chain 'D' and resid 2082 through 2099 Processing helix chain 'D' and resid 2109 through 2115 Processing helix chain 'D' and resid 2118 through 2138 removed outlier: 3.562A pdb=" N TYR D2129 " --> pdb=" O ILE D2125 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D2130 " --> pdb=" O LYS D2126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP D2138 " --> pdb=" O VAL D2134 " (cutoff:3.500A) Processing helix chain 'D' and resid 2149 through 2166 removed outlier: 4.236A pdb=" N ARG D2165 " --> pdb=" O HIS D2161 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N HIS D2166 " --> pdb=" O GLN D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2168 through 2174 Processing helix chain 'D' and resid 2183 through 2190 Processing helix chain 'D' and resid 2214 through 2217 removed outlier: 3.561A pdb=" N GLU D2217 " --> pdb=" O SER D2214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2214 through 2217' Processing helix chain 'D' and resid 2221 through 2230 Processing helix chain 'D' and resid 2240 through 2262 removed outlier: 3.537A pdb=" N ARG D2246 " --> pdb=" O ASP D2242 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D2247 " --> pdb=" O PHE D2243 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU D2248 " --> pdb=" O PHE D2244 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP D2249 " --> pdb=" O LEU D2245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D2261 " --> pdb=" O GLN D2257 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA D2262 " --> pdb=" O LYS D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2264 through 2270 removed outlier: 3.576A pdb=" N TRP D2268 " --> pdb=" O PRO D2264 " (cutoff:3.500A) Processing helix chain 'D' and resid 2273 through 2293 Processing helix chain 'D' and resid 2329 through 2347 Processing helix chain 'D' and resid 2351 through 2376 Processing helix chain 'D' and resid 2378 through 2381 Processing helix chain 'D' and resid 2383 through 2388 Processing helix chain 'D' and resid 2391 through 2407 Processing helix chain 'D' and resid 2410 through 2423 Processing helix chain 'D' and resid 2425 through 2435 removed outlier: 4.038A pdb=" N VAL D2434 " --> pdb=" O VAL D2430 " (cutoff:3.500A) Processing helix chain 'D' and resid 2438 through 2462 Processing helix chain 'D' and resid 2464 through 2466 No H-bonds generated for 'chain 'D' and resid 2464 through 2466' Processing helix chain 'D' and resid 2531 through 2541 Processing helix chain 'D' and resid 2549 through 2551 No H-bonds generated for 'chain 'D' and resid 2549 through 2551' Processing helix chain 'D' and resid 2563 through 2577 Processing helix chain 'D' and resid 2581 through 2608 removed outlier: 3.895A pdb=" N ARG D2597 " --> pdb=" O PHE D2593 " (cutoff:3.500A) Processing helix chain 'D' and resid 2618 through 2621 Processing helix chain 'D' and resid 2628 through 2634 removed outlier: 3.666A pdb=" N LYS D2633 " --> pdb=" O GLU D2629 " (cutoff:3.500A) Processing helix chain 'D' and resid 2638 through 2650 Processing helix chain 'D' and resid 2653 through 2655 No H-bonds generated for 'chain 'D' and resid 2653 through 2655' Processing helix chain 'D' and resid 2658 through 2668 Processing helix chain 'D' and resid 2689 through 2736 removed outlier: 3.540A pdb=" N THR D2710 " --> pdb=" O LYS D2707 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D2736 " --> pdb=" O ILE D2733 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 122 through 125 removed outlier: 5.791A pdb=" N SER A 16 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU A 222 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR A 18 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE A 220 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU A 20 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TRP A 218 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 29 removed outlier: 4.291A pdb=" N PHE A 26 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 40 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 240 through 244 Processing sheet with id= F, first strand: chain 'A' and resid 251 through 256 Processing sheet with id= G, first strand: chain 'A' and resid 282 through 286 Processing sheet with id= H, first strand: chain 'A' and resid 313 through 318 removed outlier: 3.576A pdb=" N SER A 354 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 368 through 372 Processing sheet with id= J, first strand: chain 'A' and resid 398 through 401 Processing sheet with id= K, first strand: chain 'A' and resid 669 through 672 Processing sheet with id= L, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 3.648A pdb=" N LYS A1196 " --> pdb=" O GLN A1189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2193 through 2199 Processing sheet with id= N, first strand: chain 'A' and resid 2468 through 2471 Processing sheet with id= O, first strand: chain 'A' and resid 131 through 139 removed outlier: 3.582A pdb=" N ARG A 148 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 122 through 125 removed outlier: 5.791A pdb=" N SER B 16 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU B 222 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR B 18 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE B 220 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU B 20 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TRP B 218 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 26 through 29 removed outlier: 4.290A pdb=" N PHE B 26 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 40 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= S, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= T, first strand: chain 'B' and resid 240 through 244 Processing sheet with id= U, first strand: chain 'B' and resid 251 through 256 Processing sheet with id= V, first strand: chain 'B' and resid 282 through 286 Processing sheet with id= W, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.576A pdb=" N SER B 354 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 368 through 372 Processing sheet with id= Y, first strand: chain 'B' and resid 398 through 401 Processing sheet with id= Z, first strand: chain 'B' and resid 669 through 672 Processing sheet with id= AA, first strand: chain 'B' and resid 1188 through 1190 removed outlier: 3.648A pdb=" N LYS B1196 " --> pdb=" O GLN B1189 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 2193 through 2199 Processing sheet with id= AC, first strand: chain 'B' and resid 2468 through 2471 Processing sheet with id= AD, first strand: chain 'B' and resid 131 through 139 removed outlier: 3.582A pdb=" N ARG B 148 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 122 through 125 removed outlier: 5.792A pdb=" N SER C 16 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU C 222 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 18 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE C 220 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU C 20 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TRP C 218 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 26 through 29 removed outlier: 4.291A pdb=" N PHE C 26 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 40 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= AH, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AI, first strand: chain 'C' and resid 240 through 244 Processing sheet with id= AJ, first strand: chain 'C' and resid 251 through 256 Processing sheet with id= AK, first strand: chain 'C' and resid 282 through 286 Processing sheet with id= AL, first strand: chain 'C' and resid 313 through 318 removed outlier: 3.576A pdb=" N SER C 354 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 368 through 372 Processing sheet with id= AN, first strand: chain 'C' and resid 398 through 401 Processing sheet with id= AO, first strand: chain 'C' and resid 669 through 672 Processing sheet with id= AP, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 3.647A pdb=" N LYS C1196 " --> pdb=" O GLN C1189 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 2193 through 2199 Processing sheet with id= AR, first strand: chain 'C' and resid 2468 through 2471 Processing sheet with id= AS, first strand: chain 'C' and resid 131 through 139 removed outlier: 3.582A pdb=" N ARG C 148 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 122 through 125 removed outlier: 5.791A pdb=" N SER D 16 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 222 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR D 18 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE D 220 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU D 20 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TRP D 218 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 26 through 29 removed outlier: 4.290A pdb=" N PHE D 26 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 40 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'D' and resid 161 through 165 Processing sheet with id= AW, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AX, first strand: chain 'D' and resid 240 through 244 Processing sheet with id= AY, first strand: chain 'D' and resid 251 through 256 Processing sheet with id= AZ, first strand: chain 'D' and resid 282 through 286 Processing sheet with id= BA, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.576A pdb=" N SER D 354 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'D' and resid 368 through 372 Processing sheet with id= BC, first strand: chain 'D' and resid 398 through 401 Processing sheet with id= BD, first strand: chain 'D' and resid 669 through 672 Processing sheet with id= BE, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.649A pdb=" N LYS D1196 " --> pdb=" O GLN D1189 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'D' and resid 2193 through 2199 Processing sheet with id= BG, first strand: chain 'D' and resid 2468 through 2471 Processing sheet with id= BH, first strand: chain 'D' and resid 131 through 139 removed outlier: 3.582A pdb=" N ARG D 148 " --> pdb=" O ASN D 135 " (cutoff:3.500A) 3924 hydrogen bonds defined for protein. 10548 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: 36.11 Time building geometry restraints manager: 27.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 25492 1.34 - 1.46: 17133 1.46 - 1.58: 35883 1.58 - 1.71: 56 1.71 - 1.83: 712 Bond restraints: 79276 Sorted by residual: bond pdb=" N VAL A1100 " pdb=" CA VAL A1100 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.25e-02 6.40e+03 1.57e+01 bond pdb=" N LEU C1102 " pdb=" CA LEU C1102 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.56e+01 bond pdb=" N LEU A1102 " pdb=" CA LEU A1102 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.54e+01 bond pdb=" N VAL C1100 " pdb=" CA VAL C1100 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.54e+01 bond pdb=" N LEU B1102 " pdb=" CA LEU B1102 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.54e+01 ... (remaining 79271 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.36: 900 104.36 - 111.81: 38511 111.81 - 119.26: 28077 119.26 - 126.71: 38527 126.71 - 134.16: 829 Bond angle restraints: 106844 Sorted by residual: angle pdb=" CA PRO A2440 " pdb=" N PRO A2440 " pdb=" CD PRO A2440 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" CA PRO D2440 " pdb=" N PRO D2440 " pdb=" CD PRO D2440 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" CA PRO B2440 " pdb=" N PRO B2440 " pdb=" CD PRO B2440 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.81e+01 angle pdb=" CA PRO C2440 " pdb=" N PRO C2440 " pdb=" CD PRO C2440 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.77e+01 angle pdb=" N GLN A1107 " pdb=" CA GLN A1107 " pdb=" C GLN A1107 " ideal model delta sigma weight residual 111.75 106.37 5.38 1.28e+00 6.10e-01 1.77e+01 ... (remaining 106839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 43381 17.86 - 35.73: 3977 35.73 - 53.59: 716 53.59 - 71.46: 142 71.46 - 89.32: 72 Dihedral angle restraints: 48288 sinusoidal: 20400 harmonic: 27888 Sorted by residual: dihedral pdb=" CA LEU D 665 " pdb=" C LEU D 665 " pdb=" N ILE D 666 " pdb=" CA ILE D 666 " ideal model delta harmonic sigma weight residual 180.00 142.01 37.99 0 5.00e+00 4.00e-02 5.77e+01 dihedral pdb=" CA LEU A 665 " pdb=" C LEU A 665 " pdb=" N ILE A 666 " pdb=" CA ILE A 666 " ideal model delta harmonic sigma weight residual 180.00 142.04 37.96 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA LEU B 665 " pdb=" C LEU B 665 " pdb=" N ILE B 666 " pdb=" CA ILE B 666 " ideal model delta harmonic sigma weight residual 180.00 142.07 37.93 0 5.00e+00 4.00e-02 5.76e+01 ... (remaining 48285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 9201 0.047 - 0.095: 2320 0.095 - 0.142: 415 0.142 - 0.190: 64 0.190 - 0.237: 20 Chirality restraints: 12020 Sorted by residual: chirality pdb=" CB THR D2625 " pdb=" CA THR D2625 " pdb=" OG1 THR D2625 " pdb=" CG2 THR D2625 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C6 PLX C5110 " pdb=" C7 PLX C5110 " pdb=" O6 PLX C5110 " pdb=" O7 PLX C5110 " both_signs ideal model delta sigma weight residual False 2.32 2.09 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C6 PLX D5108 " pdb=" C7 PLX D5108 " pdb=" O6 PLX D5108 " pdb=" O7 PLX D5108 " both_signs ideal model delta sigma weight residual False 2.32 2.09 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 12017 not shown) Planarity restraints: 13576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B1098 " 0.048 2.00e-02 2.50e+03 9.49e-02 9.01e+01 pdb=" C LYS B1098 " -0.164 2.00e-02 2.50e+03 pdb=" O LYS B1098 " 0.062 2.00e-02 2.50e+03 pdb=" N GLN B1099 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1098 " -0.048 2.00e-02 2.50e+03 9.49e-02 9.00e+01 pdb=" C LYS C1098 " 0.164 2.00e-02 2.50e+03 pdb=" O LYS C1098 " -0.062 2.00e-02 2.50e+03 pdb=" N GLN C1099 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1098 " 0.048 2.00e-02 2.50e+03 9.48e-02 8.98e+01 pdb=" C LYS A1098 " -0.164 2.00e-02 2.50e+03 pdb=" O LYS A1098 " 0.062 2.00e-02 2.50e+03 pdb=" N GLN A1099 " 0.054 2.00e-02 2.50e+03 ... (remaining 13573 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 3258 2.72 - 3.27: 81230 3.27 - 3.81: 128346 3.81 - 4.36: 151099 4.36 - 4.90: 258756 Nonbonded interactions: 622689 Sorted by model distance: nonbonded pdb=" O LEU A 895 " pdb=" ND1 HIS A 899 " model vdw 2.177 2.520 nonbonded pdb=" O LEU B 895 " pdb=" ND1 HIS B 899 " model vdw 2.177 2.520 nonbonded pdb=" O LEU D 895 " pdb=" ND1 HIS D 899 " model vdw 2.177 2.520 nonbonded pdb=" O LEU C 895 " pdb=" ND1 HIS C 899 " model vdw 2.177 2.520 nonbonded pdb=" O THR D 276 " pdb=" NZ LYS D 508 " model vdw 2.197 2.520 ... (remaining 622684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 2638 or resid 2640 through 2739 or resid 5101 th \ rough 5105 or (resid 5108 and (name C1 or name C10 or name C11 or name C12 or na \ me C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or \ name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5109 and (name \ C1 or name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or n \ ame C2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or \ name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or na \ me P1 )) or (resid 5110 through 5112 and (name C1 or name C10 or name C11 or nam \ e C12 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or na \ me O8 or name O9 or name P1 )))) selection = (chain 'B' and (resid 5 through 2638 or resid 2640 through 2739 or resid 5101 th \ rough 5105 or (resid 5108 and (name C1 or name C10 or name C11 or name C12 or na \ me C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or \ name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5109 and (name \ C1 or name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or n \ ame C2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or \ name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or na \ me P1 )) or (resid 5110 through 5112 and (name C1 or name C10 or name C11 or nam \ e C12 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or na \ me O8 or name O9 or name P1 )))) selection = (chain 'C' and (resid 5 through 2638 or resid 2640 through 2739 or resid 5101 th \ rough 5105 or (resid 5108 and (name C1 or name C10 or name C11 or name C12 or na \ me C13 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or \ name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5109 and (name \ C1 or name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or n \ ame C2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or \ name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or na \ me P1 )) or (resid 5110 through 5112 and (name C1 or name C10 or name C11 or nam \ e C12 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or na \ me O8 or name O9 or name P1 )))) selection = (chain 'D' and (resid 5 through 2638 or resid 2640 through 2739 or resid 5101 th \ rough 5105 or resid 5108 through 5109 or (resid 5110 through 5112 and (name C1 o \ r name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C \ 2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or nam \ e C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O \ 4 or name O6 or name O7 or name O8 or name O9 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 20 9.91 5 Zn 4 6.06 5 P 28 5.49 5 S 472 5.16 5 C 49600 2.51 5 N 13312 2.21 5 O 14492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 12.970 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.530 Process input model: 208.810 Find NCS groups from input model: 6.350 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.004 0.081 79276 Z= 0.261 Angle : 0.642 12.778 106844 Z= 0.331 Chirality : 0.043 0.237 12020 Planarity : 0.005 0.132 13576 Dihedral : 14.299 89.323 30116 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.15 % Favored : 95.47 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 9404 helix: 1.62 (0.07), residues: 5680 sheet: -0.18 (0.21), residues: 660 loop : -0.82 (0.12), residues: 3064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 956 time to evaluate : 7.154 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 984 average time/residue: 0.7395 time to fit residues: 1229.1491 Evaluate side-chains 656 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 644 time to evaluate : 6.703 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5819 time to fit residues: 22.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 3.9990 chunk 718 optimal weight: 8.9990 chunk 398 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 484 optimal weight: 7.9990 chunk 383 optimal weight: 7.9990 chunk 743 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 451 optimal weight: 1.9990 chunk 553 optimal weight: 4.9990 chunk 860 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 ASN A2601 GLN B 564 GLN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 HIS ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1463 ASN ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2053 ASN B2601 GLN C 564 GLN ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 HIS ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1463 ASN ** C1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2053 ASN C2601 GLN D 564 GLN ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 HIS ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1463 ASN ** D1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2053 ASN D2601 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 79276 Z= 0.462 Angle : 0.759 14.897 106844 Z= 0.384 Chirality : 0.047 0.279 12020 Planarity : 0.006 0.103 13576 Dihedral : 8.144 59.689 10840 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.17 % Favored : 94.53 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 9404 helix: 0.95 (0.07), residues: 5640 sheet: -0.36 (0.21), residues: 632 loop : -0.92 (0.11), residues: 3132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 689 time to evaluate : 6.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 18 residues processed: 719 average time/residue: 0.7294 time to fit residues: 912.1190 Evaluate side-chains 594 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 576 time to evaluate : 6.699 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5676 time to fit residues: 29.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 0.3980 chunk 267 optimal weight: 2.9990 chunk 716 optimal weight: 0.8980 chunk 586 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 862 optimal weight: 10.0000 chunk 931 optimal weight: 0.7980 chunk 768 optimal weight: 0.9980 chunk 855 optimal weight: 8.9990 chunk 294 optimal weight: 0.8980 chunk 691 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN A 609 HIS ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A1511 GLN ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 609 HIS ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1511 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 GLN C 609 HIS ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1463 ASN C1511 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN D 609 HIS ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1463 ASN D1511 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 79276 Z= 0.165 Angle : 0.578 12.951 106844 Z= 0.291 Chirality : 0.040 0.174 12020 Planarity : 0.005 0.103 13576 Dihedral : 7.223 59.701 10840 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.93 % Favored : 95.82 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 9404 helix: 1.31 (0.07), residues: 5656 sheet: -0.31 (0.20), residues: 696 loop : -0.82 (0.12), residues: 3052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 695 time to evaluate : 6.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 16 residues processed: 721 average time/residue: 0.7091 time to fit residues: 891.5493 Evaluate side-chains 626 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 610 time to evaluate : 6.732 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6094 time to fit residues: 27.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 40.0000 chunk 648 optimal weight: 6.9990 chunk 447 optimal weight: 5.9990 chunk 95 optimal weight: 0.3980 chunk 411 optimal weight: 6.9990 chunk 579 optimal weight: 20.0000 chunk 865 optimal weight: 10.0000 chunk 916 optimal weight: 8.9990 chunk 452 optimal weight: 0.0470 chunk 820 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 overall best weight: 3.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 ASN A2151 ASN ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2053 ASN B2308 HIS ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1297 HIS ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2053 ASN C2308 HIS ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1297 HIS ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2053 ASN D2308 HIS ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 79276 Z= 0.342 Angle : 0.659 15.346 106844 Z= 0.331 Chirality : 0.043 0.203 12020 Planarity : 0.005 0.103 13576 Dihedral : 7.502 59.392 10840 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.11 % Favored : 94.65 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 9404 helix: 1.07 (0.07), residues: 5668 sheet: -0.52 (0.20), residues: 684 loop : -0.96 (0.12), residues: 3052 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 641 time to evaluate : 6.940 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: 47 outliers final: 13 residues processed: 658 average time/residue: 0.7315 time to fit residues: 836.9080 Evaluate side-chains 609 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 596 time to evaluate : 6.759 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5609 time to fit residues: 23.5339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 8.9990 chunk 520 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 682 optimal weight: 0.8980 chunk 378 optimal weight: 40.0000 chunk 781 optimal weight: 2.9990 chunk 633 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 467 optimal weight: 0.0370 chunk 822 optimal weight: 0.4980 chunk 231 optimal weight: 0.2980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A2151 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2154 HIS ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.081 79276 Z= 0.147 Angle : 0.557 12.935 106844 Z= 0.281 Chirality : 0.039 0.166 12020 Planarity : 0.004 0.103 13576 Dihedral : 6.803 58.529 10840 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.89 % Favored : 95.89 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 9404 helix: 1.32 (0.07), residues: 5696 sheet: -0.36 (0.19), residues: 724 loop : -0.89 (0.12), residues: 2984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 717 time to evaluate : 7.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 10 residues processed: 749 average time/residue: 0.7233 time to fit residues: 944.7848 Evaluate side-chains 628 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 618 time to evaluate : 6.757 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5667 time to fit residues: 20.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 9.9990 chunk 825 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 538 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 917 optimal weight: 4.9990 chunk 761 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 481 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 507 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A1375 HIS ** A1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 ASN A2308 HIS ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2053 ASN B2151 ASN ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2053 ASN ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2053 ASN ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 79276 Z= 0.369 Angle : 0.676 15.842 106844 Z= 0.340 Chirality : 0.044 0.196 12020 Planarity : 0.005 0.104 13576 Dihedral : 7.366 59.401 10840 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.09), residues: 9404 helix: 1.05 (0.07), residues: 5664 sheet: -0.58 (0.20), residues: 692 loop : -1.05 (0.11), residues: 3048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 634 time to evaluate : 6.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 18 residues processed: 669 average time/residue: 0.7325 time to fit residues: 855.1918 Evaluate side-chains 615 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 597 time to evaluate : 6.764 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6097 time to fit residues: 29.7984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 522 optimal weight: 0.9990 chunk 669 optimal weight: 3.9990 chunk 518 optimal weight: 3.9990 chunk 772 optimal weight: 0.2980 chunk 512 optimal weight: 0.0770 chunk 913 optimal weight: 5.9990 chunk 571 optimal weight: 3.9990 chunk 557 optimal weight: 4.9990 chunk 421 optimal weight: 0.3980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2151 ASN ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2151 ASN ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1297 HIS ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1297 HIS ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.081 79276 Z= 0.151 Angle : 0.571 13.771 106844 Z= 0.286 Chirality : 0.039 0.166 12020 Planarity : 0.004 0.104 13576 Dihedral : 6.711 57.875 10840 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.87 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 9404 helix: 1.33 (0.07), residues: 5680 sheet: -0.34 (0.19), residues: 732 loop : -0.87 (0.12), residues: 2992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 671 time to evaluate : 6.950 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 outliers start: 30 outliers final: 21 residues processed: 694 average time/residue: 0.7484 time to fit residues: 906.9924 Evaluate side-chains 634 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 613 time to evaluate : 6.727 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5724 time to fit residues: 32.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 275 optimal weight: 0.0020 chunk 179 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 622 optimal weight: 5.9990 chunk 451 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 718 optimal weight: 5.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2151 ASN ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 HIS ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 79276 Z= 0.424 Angle : 0.711 15.499 106844 Z= 0.355 Chirality : 0.045 0.213 12020 Planarity : 0.005 0.104 13576 Dihedral : 7.332 59.997 10840 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.57 % Favored : 94.21 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.09), residues: 9404 helix: 0.99 (0.07), residues: 5652 sheet: -0.52 (0.19), residues: 700 loop : -1.08 (0.11), residues: 3052 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 625 time to evaluate : 6.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 652 average time/residue: 0.7535 time to fit residues: 858.4586 Evaluate side-chains 630 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 609 time to evaluate : 6.784 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6224 time to fit residues: 34.2438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 10.0000 chunk 875 optimal weight: 0.8980 chunk 798 optimal weight: 0.9980 chunk 851 optimal weight: 30.0000 chunk 512 optimal weight: 0.7980 chunk 370 optimal weight: 7.9990 chunk 668 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 769 optimal weight: 6.9990 chunk 805 optimal weight: 2.9990 chunk 848 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2151 ASN ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 HIS ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1275 HIS ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2151 ASN ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2115 ASN ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1275 HIS ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2308 HIS ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 79276 Z= 0.180 Angle : 0.595 13.927 106844 Z= 0.298 Chirality : 0.040 0.215 12020 Planarity : 0.005 0.104 13576 Dihedral : 6.845 59.930 10840 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.21 % Favored : 95.57 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 9404 helix: 1.28 (0.07), residues: 5660 sheet: -0.32 (0.20), residues: 696 loop : -0.95 (0.12), residues: 3048 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 647 time to evaluate : 6.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 651 average time/residue: 0.7368 time to fit residues: 832.3682 Evaluate side-chains 609 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 600 time to evaluate : 6.873 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6093 time to fit residues: 20.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 20.0000 chunk 900 optimal weight: 5.9990 chunk 549 optimal weight: 0.9980 chunk 427 optimal weight: 2.9990 chunk 625 optimal weight: 10.0000 chunk 944 optimal weight: 5.9990 chunk 869 optimal weight: 8.9990 chunk 752 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 580 optimal weight: 10.0000 chunk 461 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2151 ASN ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2151 ASN ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 79276 Z= 0.254 Angle : 0.624 15.314 106844 Z= 0.311 Chirality : 0.041 0.217 12020 Planarity : 0.005 0.104 13576 Dihedral : 6.895 59.532 10840 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.73 % Favored : 95.05 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 9404 helix: 1.27 (0.07), residues: 5624 sheet: -0.43 (0.19), residues: 696 loop : -0.94 (0.12), residues: 3084 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18808 Ramachandran restraints generated. 9404 Oldfield, 0 Emsley, 9404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 626 time to evaluate : 6.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 629 average time/residue: 0.7549 time to fit residues: 829.7501 Evaluate side-chains 609 residues out of total 8608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 605 time to evaluate : 6.767 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5948 time to fit residues: 14.4814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 6.9990 chunk 801 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 693 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 753 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 773 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2308 HIS ** B2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1275 HIS ** C1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2308 HIS ** C2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.176691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144919 restraints weight = 147828.386| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.21 r_work: 0.3682 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4284 r_free = 0.4284 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4284 r_free = 0.4284 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 79276 Z= 0.195 Angle : 0.592 13.493 106844 Z= 0.296 Chirality : 0.040 0.202 12020 Planarity : 0.004 0.104 13576 Dihedral : 6.737 59.258 10840 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.38 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 9404 helix: 1.33 (0.07), residues: 5648 sheet: -0.40 (0.19), residues: 704 loop : -0.90 (0.12), residues: 3052 =============================================================================== Job complete usr+sys time: 16803.00 seconds wall clock time: 297 minutes 32.86 seconds (17852.86 seconds total)