Starting phenix.real_space_refine on Sat Dec 9 03:17:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k32_9907/12_2023/6k32_9907_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 2.237 sd= 16.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 2 5.21 5 S 242 5.16 5 C 38758 2.51 5 N 10636 2.21 5 O 11711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A ARG 950": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "A ARG 1175": "NH1" <-> "NH2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 1116": "NH1" <-> "NH2" Residue "C ARG 1255": "NH1" <-> "NH2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 1003": "NH1" <-> "NH2" Residue "D ARG 1116": "NH1" <-> "NH2" Residue "D ARG 1255": "NH1" <-> "NH2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1116": "NH1" <-> "NH2" Residue "E ARG 1255": "NH1" <-> "NH2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F ARG 1116": "NH1" <-> "NH2" Residue "F ARG 1255": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "G TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1116": "NH1" <-> "NH2" Residue "G ARG 1255": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 61364 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9652 Classifications: {'peptide': 1208} Link IDs: {'CIS': 8, 'PTRANS': 37, 'TRANS': 1162} Chain: "B" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3981 Classifications: {'peptide': 498} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 475} Chain breaks: 2 Chain: "t" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "p" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'3PO': 1} Inner-chain residues flagged as termini: ['pdbres=" A p 2 "'] Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="3PO p 1 " pdbres=" A p 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 9622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9622 Classifications: {'peptide': 1220} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 59, 'TRANS': 1152} Chain: "D" Number of atoms: 9447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9447 Classifications: {'peptide': 1197} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 59, 'TRANS': 1133} Chain breaks: 1 Chain: "E" Number of atoms: 9402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9402 Classifications: {'peptide': 1191} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 58, 'TRANS': 1129} Chain breaks: 1 Chain: "F" Number of atoms: 9402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9402 Classifications: {'peptide': 1191} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 58, 'TRANS': 1129} Chain breaks: 1 Chain: "G" Number of atoms: 9618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9618 Classifications: {'peptide': 1218} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 61, 'TRANS': 1152} Chain breaks: 1 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {' MG': 2, 'DPO': 1, 'MG7%rna3p': 1, 'UTP': 1} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 23.76, per 1000 atoms: 0.39 Number of scatterers: 61364 At special positions: 0 Unit cell: (262.89, 281.94, 217.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 242 16.00 P 15 15.00 Mg 2 11.99 O 11711 8.00 N 10636 7.00 C 38758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM13744 O3B 3PO p 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM13744 O3B 3PO p 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.76 Conformation dependent library (CDL) restraints added in 9.2 seconds 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 69 sheets defined 33.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.62 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.757A pdb=" N ALA A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 129 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS A 134 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.661A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 203 through 219 removed outlier: 4.380A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.636A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.754A pdb=" N LYS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 4.102A pdb=" N LEU A 261 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.664A pdb=" N SER A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.506A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.912A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.611A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.783A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.780A pdb=" N SER A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.918A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 557 through 573 removed outlier: 4.111A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 647 through 666 removed outlier: 3.763A pdb=" N LEU A 651 " --> pdb=" O HIS A 647 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 706 removed outlier: 4.030A pdb=" N SER A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 755 through 767 removed outlier: 3.702A pdb=" N LEU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 786 removed outlier: 3.589A pdb=" N PHE A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 removed outlier: 3.648A pdb=" N ASP A 802 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 871 through 877 removed outlier: 3.907A pdb=" N LEU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 887 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.654A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 923 removed outlier: 3.502A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 937 Processing helix chain 'A' and resid 947 through 959 Processing helix chain 'A' and resid 971 through 984 removed outlier: 4.212A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER A 980 " --> pdb=" O LYS A 976 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1006 removed outlier: 3.769A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1068 through 1076 removed outlier: 4.302A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.622A pdb=" N ILE A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1118 through 1132 removed outlier: 3.695A pdb=" N LEU A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1174 through 1188 removed outlier: 3.639A pdb=" N ASN A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A1186 " --> pdb=" O SER A1182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1187 " --> pdb=" O TYR A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.519A pdb=" N VAL A1210 " --> pdb=" O LEU A1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.520A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.764A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.815A pdb=" N MET B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.563A pdb=" N ALA B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 143 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.970A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.552A pdb=" N PHE B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.938A pdb=" N ALA B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.661A pdb=" N ALA B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.738A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 392' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.617A pdb=" N MET B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.725A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.871A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 456 " --> pdb=" O MET B 452 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 removed outlier: 3.754A pdb=" N SER B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 524 through 537 removed outlier: 4.058A pdb=" N LEU B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 removed outlier: 4.102A pdb=" N LYS B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 124 No H-bonds generated for 'chain 'C' and resid 121 through 124' Processing helix chain 'C' and resid 126 through 129 No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 184 through 187 No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 244 through 259 removed outlier: 4.283A pdb=" N VAL C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 308 through 318 removed outlier: 4.173A pdb=" N MET C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.777A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.629A pdb=" N ILE C 376 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 377 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 380 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.627A pdb=" N ILE C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.956A pdb=" N GLU C 423 " --> pdb=" O PRO C 420 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 427 " --> pdb=" O GLY C 424 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 431 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 435 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 471 removed outlier: 4.031A pdb=" N ALA C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 485 removed outlier: 4.038A pdb=" N ALA C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 520 removed outlier: 3.507A pdb=" N ILE C 508 " --> pdb=" O PRO C 505 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 509 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 510 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 515 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 516 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 517 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE C 520 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 527 Processing helix chain 'C' and resid 529 through 543 removed outlier: 3.987A pdb=" N LEU C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 removed outlier: 3.538A pdb=" N GLY C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 554 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 598 through 604 Processing helix chain 'C' and resid 617 through 620 No H-bonds generated for 'chain 'C' and resid 617 through 620' Processing helix chain 'C' and resid 651 through 667 removed outlier: 3.729A pdb=" N THR C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 664 " --> pdb=" O ALA C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 684 removed outlier: 4.040A pdb=" N THR C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 683 " --> pdb=" O CYS C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 701 removed outlier: 3.822A pdb=" N ILE C 694 " --> pdb=" O GLN C 690 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 696 " --> pdb=" O ASP C 692 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 764 through 767 No H-bonds generated for 'chain 'C' and resid 764 through 767' Processing helix chain 'C' and resid 773 through 776 No H-bonds generated for 'chain 'C' and resid 773 through 776' Processing helix chain 'C' and resid 796 through 807 removed outlier: 4.279A pdb=" N LEU C 800 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER C 801 " --> pdb=" O THR C 798 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 802 " --> pdb=" O THR C 799 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 804 " --> pdb=" O SER C 801 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C 805 " --> pdb=" O GLN C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 removed outlier: 4.061A pdb=" N ILE C 820 " --> pdb=" O PRO C 816 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY C 826 " --> pdb=" O MET C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 3.814A pdb=" N SER C 857 " --> pdb=" O ASP C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.915A pdb=" N ILE C 865 " --> pdb=" O GLU C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 887 Processing helix chain 'C' and resid 904 through 912 removed outlier: 3.733A pdb=" N TYR C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 962 through 970 removed outlier: 3.582A pdb=" N GLN C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 removed outlier: 3.510A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1002 Processing helix chain 'C' and resid 1038 through 1040 No H-bonds generated for 'chain 'C' and resid 1038 through 1040' Processing helix chain 'C' and resid 1049 through 1062 removed outlier: 3.852A pdb=" N ARG C1053 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C1060 " --> pdb=" O SER C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1162 removed outlier: 3.546A pdb=" N ILE C1156 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1190 through 1194 Processing helix chain 'C' and resid 1325 through 1327 No H-bonds generated for 'chain 'C' and resid 1325 through 1327' Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'D' and resid 191 through 194 No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 244 through 259 removed outlier: 3.603A pdb=" N TYR D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 248 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 254 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 257 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 352 through 363 removed outlier: 3.599A pdb=" N VAL D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 382 removed outlier: 3.609A pdb=" N GLN D 380 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.648A pdb=" N ARG D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 437 removed outlier: 4.166A pdb=" N GLU D 423 " --> pdb=" O PRO D 420 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL D 427 " --> pdb=" O GLY D 424 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 429 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 431 " --> pdb=" O GLN D 428 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 435 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 removed outlier: 4.295A pdb=" N ARG D 461 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL D 463 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 464 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 466 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 468 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.652A pdb=" N HIS D 479 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL D 486 " --> pdb=" O ILE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 520 removed outlier: 3.810A pdb=" N VAL D 510 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 512 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 515 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 516 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 519 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 520 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 529 through 543 removed outlier: 4.489A pdb=" N LEU D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.530A pdb=" N GLY D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 588 through 590 No H-bonds generated for 'chain 'D' and resid 588 through 590' Processing helix chain 'D' and resid 600 through 604 Processing helix chain 'D' and resid 617 through 621 Processing helix chain 'D' and resid 649 through 669 removed outlier: 4.102A pdb=" N ASN D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 684 Processing helix chain 'D' and resid 686 through 701 removed outlier: 3.660A pdb=" N ILE D 694 " --> pdb=" O GLN D 690 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 696 " --> pdb=" O ASP D 692 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP D 700 " --> pdb=" O VAL D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 709 Processing helix chain 'D' and resid 760 through 767 removed outlier: 3.878A pdb=" N VAL D 763 " --> pdb=" O THR D 760 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP D 764 " --> pdb=" O SER D 761 " (cutoff:3.500A) Proline residue: D 765 - end of helix No H-bonds generated for 'chain 'D' and resid 760 through 767' Processing helix chain 'D' and resid 797 through 807 removed outlier: 3.571A pdb=" N SER D 803 " --> pdb=" O THR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 823 removed outlier: 3.545A pdb=" N ASN D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET D 822 " --> pdb=" O ALA D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 858 removed outlier: 3.693A pdb=" N HIS D 858 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 904 through 909 removed outlier: 3.587A pdb=" N TYR D 909 " --> pdb=" O SER D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 951 No H-bonds generated for 'chain 'D' and resid 948 through 951' Processing helix chain 'D' and resid 962 through 970 removed outlier: 3.749A pdb=" N GLN D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 989 removed outlier: 3.709A pdb=" N GLN D 988 " --> pdb=" O GLU D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1004 Processing helix chain 'D' and resid 1038 through 1040 No H-bonds generated for 'chain 'D' and resid 1038 through 1040' Processing helix chain 'D' and resid 1049 through 1062 removed outlier: 4.066A pdb=" N ARG D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D1060 " --> pdb=" O SER D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1149 through 1162 removed outlier: 3.689A pdb=" N ILE D1156 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1190 through 1194 removed outlier: 3.537A pdb=" N MET D1194 " --> pdb=" O ALA D1190 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1190 through 1194' Processing helix chain 'E' and resid 184 through 187 No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 191 through 194 No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 244 through 259 removed outlier: 3.617A pdb=" N TYR E 247 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 248 " --> pdb=" O ALA E 245 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 254 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 256 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 258 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET E 259 " --> pdb=" O PHE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.540A pdb=" N LEU E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.816A pdb=" N MET E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 363 removed outlier: 3.509A pdb=" N VAL E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 395 through 397 No H-bonds generated for 'chain 'E' and resid 395 through 397' Processing helix chain 'E' and resid 405 through 418 removed outlier: 3.804A pdb=" N ARG E 410 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 437 removed outlier: 3.928A pdb=" N GLU E 423 " --> pdb=" O PRO E 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL E 427 " --> pdb=" O GLY E 424 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 431 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E 435 " --> pdb=" O GLY E 432 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 436 " --> pdb=" O TYR E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 469 removed outlier: 3.969A pdb=" N ALA E 465 " --> pdb=" O ARG E 461 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA E 468 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 486 removed outlier: 3.822A pdb=" N GLU E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL E 486 " --> pdb=" O ILE E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 removed outlier: 3.568A pdb=" N ILE E 508 " --> pdb=" O PRO E 505 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 509 " --> pdb=" O SER E 506 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 510 " --> pdb=" O SER E 507 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 515 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 516 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 517 " --> pdb=" O PHE E 514 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 519 " --> pdb=" O LEU E 516 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE E 520 " --> pdb=" O PHE E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 529 through 543 removed outlier: 3.532A pdb=" N ASN E 534 " --> pdb=" O GLY E 530 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 535 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 538 " --> pdb=" O ASN E 534 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 542 " --> pdb=" O LEU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.717A pdb=" N GLY E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 550 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 554 " --> pdb=" O ILE E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 587 through 589 No H-bonds generated for 'chain 'E' and resid 587 through 589' Processing helix chain 'E' and resid 598 through 607 removed outlier: 4.468A pdb=" N LEU E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE E 607 " --> pdb=" O ILE E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 621 Processing helix chain 'E' and resid 649 through 669 removed outlier: 3.630A pdb=" N THR E 658 " --> pdb=" O THR E 654 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN E 661 " --> pdb=" O ALA E 657 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 665 " --> pdb=" O ASN E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 684 removed outlier: 3.699A pdb=" N THR E 680 " --> pdb=" O THR E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 709 removed outlier: 3.876A pdb=" N ILE E 694 " --> pdb=" O GLN E 690 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL E 696 " --> pdb=" O ASP E 692 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER E 703 " --> pdb=" O THR E 699 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL E 704 " --> pdb=" O ASP E 700 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 705 " --> pdb=" O HIS E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 767 removed outlier: 3.686A pdb=" N VAL E 763 " --> pdb=" O THR E 760 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP E 764 " --> pdb=" O SER E 761 " (cutoff:3.500A) Proline residue: E 765 - end of helix No H-bonds generated for 'chain 'E' and resid 760 through 767' Processing helix chain 'E' and resid 797 through 809 removed outlier: 3.750A pdb=" N GLN E 802 " --> pdb=" O THR E 798 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 823 removed outlier: 4.129A pdb=" N ILE E 820 " --> pdb=" O PRO E 816 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN E 821 " --> pdb=" O ASP E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 858 Processing helix chain 'E' and resid 860 through 862 No H-bonds generated for 'chain 'E' and resid 860 through 862' Processing helix chain 'E' and resid 880 through 889 Processing helix chain 'E' and resid 904 through 912 removed outlier: 4.014A pdb=" N TYR E 909 " --> pdb=" O SER E 905 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 912 " --> pdb=" O THR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 928 No H-bonds generated for 'chain 'E' and resid 926 through 928' Processing helix chain 'E' and resid 948 through 950 No H-bonds generated for 'chain 'E' and resid 948 through 950' Processing helix chain 'E' and resid 962 through 970 removed outlier: 3.529A pdb=" N ALA E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 989 Processing helix chain 'E' and resid 998 through 1002 Processing helix chain 'E' and resid 1038 through 1040 No H-bonds generated for 'chain 'E' and resid 1038 through 1040' Processing helix chain 'E' and resid 1051 through 1062 removed outlier: 3.542A pdb=" N SER E1056 " --> pdb=" O LEU E1052 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E1057 " --> pdb=" O ARG E1053 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG E1060 " --> pdb=" O SER E1056 " (cutoff:3.500A) Processing helix chain 'E' and resid 1149 through 1162 removed outlier: 3.588A pdb=" N ILE E1156 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing helix chain 'E' and resid 1209 through 1211 No H-bonds generated for 'chain 'E' and resid 1209 through 1211' Processing helix chain 'E' and resid 1262 through 1265 Processing helix chain 'F' and resid 184 through 187 No H-bonds generated for 'chain 'F' and resid 184 through 187' Processing helix chain 'F' and resid 191 through 194 No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'F' and resid 244 through 259 removed outlier: 4.297A pdb=" N VAL F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 283 No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 352 through 366 removed outlier: 3.717A pdb=" N VAL F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F 362 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 382 removed outlier: 3.923A pdb=" N GLN F 380 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 381 " --> pdb=" O ALA F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 397 No H-bonds generated for 'chain 'F' and resid 395 through 397' Processing helix chain 'F' and resid 405 through 418 removed outlier: 3.719A pdb=" N ARG F 410 " --> pdb=" O ASP F 406 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 434 removed outlier: 3.898A pdb=" N GLU F 423 " --> pdb=" O PRO F 420 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 426 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL F 427 " --> pdb=" O GLY F 424 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 431 " --> pdb=" O GLN F 428 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 433 " --> pdb=" O ASN F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 4.466A pdb=" N ARG F 461 " --> pdb=" O SER F 458 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL F 463 " --> pdb=" O ALA F 460 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER F 464 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL F 466 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 467 " --> pdb=" O SER F 464 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 468 " --> pdb=" O ALA F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 483 removed outlier: 3.958A pdb=" N LEU F 480 " --> pdb=" O SER F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 520 removed outlier: 3.585A pdb=" N ILE F 508 " --> pdb=" O PRO F 505 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL F 509 " --> pdb=" O SER F 506 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL F 510 " --> pdb=" O SER F 507 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 516 " --> pdb=" O GLU F 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE F 517 " --> pdb=" O PHE F 514 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 519 " --> pdb=" O LEU F 516 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 520 " --> pdb=" O PHE F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 527 removed outlier: 3.566A pdb=" N ARG F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 543 removed outlier: 4.168A pdb=" N LEU F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 542 " --> pdb=" O LEU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 551 removed outlier: 4.155A pdb=" N GLY F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE F 550 " --> pdb=" O VAL F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 587 through 589 No H-bonds generated for 'chain 'F' and resid 587 through 589' Processing helix chain 'F' and resid 598 through 604 Processing helix chain 'F' and resid 617 through 620 No H-bonds generated for 'chain 'F' and resid 617 through 620' Processing helix chain 'F' and resid 649 through 669 removed outlier: 3.747A pdb=" N THR F 658 " --> pdb=" O THR F 654 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN F 661 " --> pdb=" O ALA F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 709 removed outlier: 3.998A pdb=" N THR F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 688 " --> pdb=" O LEU F 684 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 689 " --> pdb=" O ARG F 685 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 694 " --> pdb=" O GLN F 690 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL F 696 " --> pdb=" O ASP F 692 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER F 703 " --> pdb=" O THR F 699 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL F 704 " --> pdb=" O ASP F 700 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL F 705 " --> pdb=" O HIS F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 767 removed outlier: 3.671A pdb=" N VAL F 763 " --> pdb=" O THR F 760 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP F 764 " --> pdb=" O SER F 761 " (cutoff:3.500A) Proline residue: F 765 - end of helix No H-bonds generated for 'chain 'F' and resid 760 through 767' Processing helix chain 'F' and resid 796 through 807 removed outlier: 3.511A pdb=" N SER F 801 " --> pdb=" O SER F 797 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER F 803 " --> pdb=" O THR F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 823 removed outlier: 4.274A pdb=" N ILE F 820 " --> pdb=" O PRO F 816 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN F 821 " --> pdb=" O ASP F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 825 through 827 No H-bonds generated for 'chain 'F' and resid 825 through 827' Processing helix chain 'F' and resid 852 through 858 Processing helix chain 'F' and resid 860 through 863 No H-bonds generated for 'chain 'F' and resid 860 through 863' Processing helix chain 'F' and resid 880 through 889 Processing helix chain 'F' and resid 904 through 911 Processing helix chain 'F' and resid 948 through 950 No H-bonds generated for 'chain 'F' and resid 948 through 950' Processing helix chain 'F' and resid 962 through 970 removed outlier: 3.806A pdb=" N GLN F 966 " --> pdb=" O ASP F 962 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 989 removed outlier: 3.580A pdb=" N ILE F 986 " --> pdb=" O ALA F 982 " (cutoff:3.500A) Processing helix chain 'F' and resid 996 through 1002 removed outlier: 3.757A pdb=" N LEU F1000 " --> pdb=" O ASP F 996 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1040 No H-bonds generated for 'chain 'F' and resid 1038 through 1040' Processing helix chain 'F' and resid 1049 through 1062 removed outlier: 4.108A pdb=" N ARG F1053 " --> pdb=" O GLU F1049 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F1057 " --> pdb=" O ARG F1053 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F1060 " --> pdb=" O SER F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1149 through 1162 removed outlier: 3.628A pdb=" N ILE F1156 " --> pdb=" O ALA F1152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F1160 " --> pdb=" O ILE F1156 " (cutoff:3.500A) Processing helix chain 'F' and resid 1209 through 1211 No H-bonds generated for 'chain 'F' and resid 1209 through 1211' Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.699A pdb=" N ASP G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 120 " --> pdb=" O SER G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 194 No H-bonds generated for 'chain 'G' and resid 191 through 194' Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 244 through 259 removed outlier: 3.528A pdb=" N VAL G 248 " --> pdb=" O ALA G 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 251 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 252 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 254 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 258 " --> pdb=" O LEU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 298 through 301 Processing helix chain 'G' and resid 308 through 318 Processing helix chain 'G' and resid 352 through 363 removed outlier: 3.779A pdb=" N VAL G 357 " --> pdb=" O PHE G 353 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 362 " --> pdb=" O LEU G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.697A pdb=" N GLN G 380 " --> pdb=" O LYS G 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA G 381 " --> pdb=" O ALA G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 397 No H-bonds generated for 'chain 'G' and resid 395 through 397' Processing helix chain 'G' and resid 405 through 418 removed outlier: 3.598A pdb=" N ILE G 409 " --> pdb=" O HIS G 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 410 " --> pdb=" O ASP G 406 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET G 413 " --> pdb=" O ILE G 409 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 416 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 417 " --> pdb=" O MET G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.919A pdb=" N GLU G 423 " --> pdb=" O PRO G 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 426 " --> pdb=" O GLU G 423 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL G 427 " --> pdb=" O GLY G 424 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 431 " --> pdb=" O GLN G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 466 removed outlier: 4.286A pdb=" N ARG G 461 " --> pdb=" O SER G 458 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 463 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER G 464 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL G 466 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 486 removed outlier: 3.755A pdb=" N LEU G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 485 " --> pdb=" O ALA G 481 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL G 486 " --> pdb=" O ILE G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 520 removed outlier: 3.745A pdb=" N ILE G 508 " --> pdb=" O PRO G 505 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL G 509 " --> pdb=" O SER G 506 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 510 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 515 " --> pdb=" O LEU G 512 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 516 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE G 517 " --> pdb=" O PHE G 514 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE G 520 " --> pdb=" O PHE G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 526 Processing helix chain 'G' and resid 529 through 543 removed outlier: 3.676A pdb=" N VAL G 535 " --> pdb=" O ASP G 531 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU G 538 " --> pdb=" O ASN G 534 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 542 " --> pdb=" O LEU G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 554 removed outlier: 3.963A pdb=" N GLY G 549 " --> pdb=" O PRO G 545 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE G 550 " --> pdb=" O VAL G 546 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE G 551 " --> pdb=" O GLU G 547 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 554 " --> pdb=" O ILE G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 590 No H-bonds generated for 'chain 'G' and resid 588 through 590' Processing helix chain 'G' and resid 598 through 604 Processing helix chain 'G' and resid 617 through 620 No H-bonds generated for 'chain 'G' and resid 617 through 620' Processing helix chain 'G' and resid 649 through 670 removed outlier: 3.520A pdb=" N THR G 654 " --> pdb=" O SER G 650 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR G 658 " --> pdb=" O THR G 654 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN G 661 " --> pdb=" O ALA G 657 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN G 664 " --> pdb=" O ALA G 660 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP G 670 " --> pdb=" O ARG G 666 " (cutoff:3.500A) Processing helix chain 'G' and resid 674 through 684 removed outlier: 3.871A pdb=" N THR G 680 " --> pdb=" O THR G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 686 through 701 removed outlier: 3.541A pdb=" N ASN G 693 " --> pdb=" O THR G 689 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 694 " --> pdb=" O GLN G 690 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL G 696 " --> pdb=" O ASP G 692 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA G 697 " --> pdb=" O ASN G 693 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP G 700 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS G 701 " --> pdb=" O ALA G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 709 Processing helix chain 'G' and resid 760 through 767 removed outlier: 3.839A pdb=" N VAL G 763 " --> pdb=" O THR G 760 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP G 764 " --> pdb=" O SER G 761 " (cutoff:3.500A) Proline residue: G 765 - end of helix No H-bonds generated for 'chain 'G' and resid 760 through 767' Processing helix chain 'G' and resid 796 through 812 removed outlier: 3.641A pdb=" N VAL G 806 " --> pdb=" O GLN G 802 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER G 811 " --> pdb=" O ALA G 807 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 812 " --> pdb=" O GLN G 808 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 removed outlier: 3.510A pdb=" N PHE G 819 " --> pdb=" O LEU G 815 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE G 820 " --> pdb=" O PRO G 816 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN G 821 " --> pdb=" O ASP G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 852 through 858 removed outlier: 3.615A pdb=" N HIS G 858 " --> pdb=" O GLN G 854 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 866 removed outlier: 3.503A pdb=" N HIS G 864 " --> pdb=" O ARG G 860 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 865 " --> pdb=" O GLU G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 880 through 889 removed outlier: 3.683A pdb=" N ALA G 885 " --> pdb=" O ASP G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 904 through 913 removed outlier: 3.532A pdb=" N THR G 908 " --> pdb=" O GLY G 904 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 909 " --> pdb=" O SER G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 948 through 950 No H-bonds generated for 'chain 'G' and resid 948 through 950' Processing helix chain 'G' and resid 962 through 970 removed outlier: 3.722A pdb=" N GLN G 966 " --> pdb=" O ASP G 962 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 967 " --> pdb=" O ALA G 963 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA G 969 " --> pdb=" O ARG G 965 " (cutoff:3.500A) Processing helix chain 'G' and resid 978 through 989 removed outlier: 3.513A pdb=" N ILE G 986 " --> pdb=" O ALA G 982 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN G 988 " --> pdb=" O GLU G 984 " (cutoff:3.500A) Processing helix chain 'G' and resid 998 through 1002 Processing helix chain 'G' and resid 1038 through 1040 No H-bonds generated for 'chain 'G' and resid 1038 through 1040' Processing helix chain 'G' and resid 1050 through 1062 removed outlier: 3.801A pdb=" N LEU G1055 " --> pdb=" O ARG G1051 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G1057 " --> pdb=" O ARG G1053 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G1060 " --> pdb=" O SER G1056 " (cutoff:3.500A) Processing helix chain 'G' and resid 1149 through 1162 removed outlier: 3.577A pdb=" N ILE G1160 " --> pdb=" O ILE G1156 " (cutoff:3.500A) Processing helix chain 'G' and resid 1262 through 1265 Processing sheet with id= A, first strand: chain 'A' and resid 54 through 57 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 185 Processing sheet with id= C, first strand: chain 'A' and resid 475 through 479 removed outlier: 4.331A pdb=" N LYS A 475 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 543 through 546 Processing sheet with id= E, first strand: chain 'A' and resid 621 through 623 Processing sheet with id= F, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.876A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 792 through 795 removed outlier: 3.631A pdb=" N SER A 829 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1022 through 1025 Processing sheet with id= I, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.841A pdb=" N ALA A 267 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.240A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 206 through 208 Processing sheet with id= L, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.609A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.710A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1300 through 1305 removed outlier: 3.753A pdb=" N ILE C 343 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 331 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 347 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 329 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 388 through 390 Processing sheet with id= P, first strand: chain 'C' and resid 440 through 442 Processing sheet with id= Q, first strand: chain 'C' and resid 558 through 560 Processing sheet with id= R, first strand: chain 'C' and resid 612 through 615 Processing sheet with id= S, first strand: chain 'C' and resid 732 through 735 Processing sheet with id= T, first strand: chain 'C' and resid 829 through 832 Processing sheet with id= U, first strand: chain 'C' and resid 833 through 835 removed outlier: 6.127A pdb=" N VAL C 917 " --> pdb=" O THR C 850 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 1230 through 1232 removed outlier: 3.501A pdb=" N VAL C1165 " --> pdb=" O VAL C1137 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C1097 " --> pdb=" O HIS C1138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR C1140 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL C1099 " --> pdb=" O THR C1140 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1107 through 1110 Processing sheet with id= X, first strand: chain 'C' and resid 1172 through 1178 removed outlier: 3.503A pdb=" N GLU C1176 " --> pdb=" O LEU C1204 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 164 through 170 removed outlier: 3.623A pdb=" N VAL C 203 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C1242 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 206 " --> pdb=" O ARG C1240 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG C1240 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.801A pdb=" N THR D 145 " --> pdb=" O VAL D1317 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 1301 through 1305 removed outlier: 3.751A pdb=" N ILE D 343 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 331 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 347 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU D 329 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 388 through 390 Processing sheet with id= AC, first strand: chain 'D' and resid 440 through 442 Processing sheet with id= AD, first strand: chain 'D' and resid 558 through 560 Processing sheet with id= AE, first strand: chain 'D' and resid 612 through 615 removed outlier: 3.519A pdb=" N ILE D 635 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 732 through 735 Processing sheet with id= AG, first strand: chain 'D' and resid 944 through 947 removed outlier: 7.805A pdb=" N VAL D 831 " --> pdb=" O THR D 851 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR D 851 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1230 through 1232 removed outlier: 6.013A pdb=" N VAL D1097 " --> pdb=" O HIS D1138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR D1140 " --> pdb=" O VAL D1097 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D1099 " --> pdb=" O THR D1140 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 1106 through 1110 Processing sheet with id= AJ, first strand: chain 'D' and resid 1172 through 1179 Processing sheet with id= AK, first strand: chain 'D' and resid 164 through 170 removed outlier: 3.679A pdb=" N VAL D 203 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET D1242 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D 206 " --> pdb=" O ARG D1240 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG D1240 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 1300 through 1305 removed outlier: 3.605A pdb=" N GLU E 331 " --> pdb=" O GLY E 345 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 347 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 329 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 388 through 390 Processing sheet with id= AN, first strand: chain 'E' and resid 558 through 560 removed outlier: 3.563A pdb=" N GLU E 567 " --> pdb=" O THR E 559 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 612 through 615 Processing sheet with id= AP, first strand: chain 'E' and resid 732 through 735 removed outlier: 3.661A pdb=" N ARG E1020 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 944 through 947 removed outlier: 7.910A pdb=" N VAL E 831 " --> pdb=" O THR E 851 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR E 851 " --> pdb=" O VAL E 831 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL E 917 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 1230 through 1232 removed outlier: 6.256A pdb=" N VAL E1097 " --> pdb=" O HIS E1138 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR E1140 " --> pdb=" O VAL E1097 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E1099 " --> pdb=" O THR E1140 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 1107 through 1110 Processing sheet with id= AT, first strand: chain 'E' and resid 1172 through 1179 Processing sheet with id= AU, first strand: chain 'E' and resid 164 through 170 removed outlier: 3.594A pdb=" N VAL E 203 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET E1242 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 206 " --> pdb=" O ARG E1240 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG E1240 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.588A pdb=" N THR F 145 " --> pdb=" O VAL F1317 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'F' and resid 1300 through 1305 removed outlier: 3.581A pdb=" N ILE F 343 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 331 " --> pdb=" O GLY F 345 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 347 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU F 329 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 388 through 390 Processing sheet with id= AY, first strand: chain 'F' and resid 558 through 560 Processing sheet with id= AZ, first strand: chain 'F' and resid 612 through 615 Processing sheet with id= BA, first strand: chain 'F' and resid 732 through 735 Processing sheet with id= BB, first strand: chain 'F' and resid 944 through 947 removed outlier: 7.755A pdb=" N VAL F 831 " --> pdb=" O THR F 851 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR F 851 " --> pdb=" O VAL F 831 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 917 " --> pdb=" O THR F 850 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 1230 through 1232 removed outlier: 6.288A pdb=" N VAL F1097 " --> pdb=" O HIS F1138 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR F1140 " --> pdb=" O VAL F1097 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F1099 " --> pdb=" O THR F1140 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 1106 through 1110 Processing sheet with id= BE, first strand: chain 'F' and resid 1176 through 1179 Processing sheet with id= BF, first strand: chain 'F' and resid 164 through 170 removed outlier: 3.873A pdb=" N MET F1242 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 206 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG F1240 " --> pdb=" O ILE F 206 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'G' and resid 145 through 147 removed outlier: 3.836A pdb=" N THR G 145 " --> pdb=" O VAL G1317 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 1300 through 1305 removed outlier: 3.811A pdb=" N ILE G 343 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU G 331 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA G 347 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU G 329 " --> pdb=" O ALA G 347 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 388 through 390 Processing sheet with id= BJ, first strand: chain 'G' and resid 584 through 586 Processing sheet with id= BK, first strand: chain 'G' and resid 612 through 615 Processing sheet with id= BL, first strand: chain 'G' and resid 732 through 735 Processing sheet with id= BM, first strand: chain 'G' and resid 944 through 947 removed outlier: 7.720A pdb=" N VAL G 831 " --> pdb=" O THR G 851 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR G 851 " --> pdb=" O VAL G 831 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL G 917 " --> pdb=" O THR G 850 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'G' and resid 1230 through 1232 removed outlier: 6.209A pdb=" N VAL G1097 " --> pdb=" O HIS G1138 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR G1140 " --> pdb=" O VAL G1097 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL G1099 " --> pdb=" O THR G1140 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'G' and resid 1107 through 1110 Processing sheet with id= BP, first strand: chain 'G' and resid 1172 through 1179 removed outlier: 3.501A pdb=" N GLU G1176 " --> pdb=" O LEU G1204 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'G' and resid 164 through 170 1401 hydrogen bonds defined for protein. 3567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.93 Time building geometry restraints manager: 20.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 3 1.14 - 1.31: 10274 1.31 - 1.48: 25564 1.48 - 1.65: 26349 1.65 - 1.82: 461 Bond restraints: 62651 Sorted by residual: bond pdb=" C TYR A1083 " pdb=" N HIS A1084 " ideal model delta sigma weight residual 1.332 1.588 -0.256 8.30e-03 1.45e+04 9.52e+02 bond pdb=" C3' MG7 A1302 " pdb=" O3' MG7 A1302 " ideal model delta sigma weight residual 1.417 0.964 0.453 1.50e-02 4.44e+03 9.12e+02 bond pdb=" C5' U t 1 " pdb=" C4' U t 1 " ideal model delta sigma weight residual 1.508 1.131 0.377 1.50e-02 4.44e+03 6.33e+02 bond pdb=" C2' MG7 A1302 " pdb=" O2' MG7 A1302 " ideal model delta sigma weight residual 1.420 1.097 0.323 1.50e-02 4.44e+03 4.62e+02 bond pdb=" C2' MG7 A1302 " pdb=" C3' MG7 A1302 " ideal model delta sigma weight residual 1.523 1.214 0.309 1.50e-02 4.44e+03 4.24e+02 ... (remaining 62646 not shown) Histogram of bond angle deviations from ideal: 68.31 - 87.26: 5 87.26 - 106.22: 1850 106.22 - 125.17: 82327 125.17 - 144.13: 1051 144.13 - 163.09: 4 Bond angle restraints: 85237 Sorted by residual: angle pdb=" O3' U t 1 " pdb=" C3' U t 1 " pdb=" C2' U t 1 " ideal model delta sigma weight residual 113.70 68.31 45.39 1.50e+00 4.44e-01 9.16e+02 angle pdb=" C5' U t 1 " pdb=" C4' U t 1 " pdb=" C3' U t 1 " ideal model delta sigma weight residual 116.00 157.03 -41.03 1.50e+00 4.44e-01 7.48e+02 angle pdb=" C4' U t 1 " pdb=" C3' U t 1 " pdb=" O3' U t 1 " ideal model delta sigma weight residual 113.00 145.42 -32.42 1.50e+00 4.44e-01 4.67e+02 angle pdb=" O2' U t 2 " pdb=" C2' U t 2 " pdb=" C1' U t 2 " ideal model delta sigma weight residual 108.40 76.66 31.74 1.50e+00 4.44e-01 4.48e+02 angle pdb=" C5' U t 1 " pdb=" C4' U t 1 " pdb=" O4' U t 1 " ideal model delta sigma weight residual 109.80 81.39 28.41 1.50e+00 4.44e-01 3.59e+02 ... (remaining 85232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 37238 30.97 - 61.94: 534 61.94 - 92.91: 86 92.91 - 123.88: 3 123.88 - 154.85: 4 Dihedral angle restraints: 37865 sinusoidal: 15144 harmonic: 22721 Sorted by residual: dihedral pdb=" CA ILE C 475 " pdb=" C ILE C 475 " pdb=" N SER C 476 " pdb=" CA SER C 476 " ideal model delta harmonic sigma weight residual -180.00 -45.47 -134.53 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA PRO A 821 " pdb=" C PRO A 821 " pdb=" N ASP A 822 " pdb=" CA ASP A 822 " ideal model delta harmonic sigma weight residual -180.00 -50.23 -129.77 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA ASN B 64 " pdb=" C ASN B 64 " pdb=" N GLY B 65 " pdb=" CA GLY B 65 " ideal model delta harmonic sigma weight residual -180.00 -58.10 -121.90 0 5.00e+00 4.00e-02 5.94e+02 ... (remaining 37862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 9734 0.396 - 0.792: 11 0.792 - 1.188: 3 1.188 - 1.584: 1 1.584 - 1.980: 3 Chirality restraints: 9752 Sorted by residual: chirality pdb=" C2' MG7 A1302 " pdb=" C1' MG7 A1302 " pdb=" C3' MG7 A1302 " pdb=" O2' MG7 A1302 " both_signs ideal model delta sigma weight residual False -2.75 -0.77 -1.98 2.00e-01 2.50e+01 9.80e+01 chirality pdb=" C4' U t 1 " pdb=" C5' U t 1 " pdb=" O4' U t 1 " pdb=" C3' U t 1 " both_signs ideal model delta sigma weight residual False -2.50 -0.85 -1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" C3' MG7 A1302 " pdb=" C2' MG7 A1302 " pdb=" C4' MG7 A1302 " pdb=" O3' MG7 A1302 " both_signs ideal model delta sigma weight residual False -2.48 -0.88 -1.60 2.00e-01 2.50e+01 6.40e+01 ... (remaining 9749 not shown) Planarity restraints: 11061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' A2M A1304 " -0.005 2.00e-02 2.50e+03 2.76e-01 1.72e+03 pdb=" C4' A2M A1304 " -0.219 2.00e-02 2.50e+03 pdb=" O4' A2M A1304 " -0.338 2.00e-02 2.50e+03 pdb=" C3' A2M A1304 " 0.394 2.00e-02 2.50e+03 pdb=" O3' A2M A1304 " 0.134 2.00e-02 2.50e+03 pdb=" C2' A2M A1304 " 0.193 2.00e-02 2.50e+03 pdb=" O2' A2M A1304 " -0.358 2.00e-02 2.50e+03 pdb=" C1' A2M A1304 " -0.189 2.00e-02 2.50e+03 pdb=" N9 A2M A1304 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UTP A1306 " 0.291 2.00e-02 2.50e+03 2.75e-01 1.70e+03 pdb=" C2' UTP A1306 " -0.144 2.00e-02 2.50e+03 pdb=" C3' UTP A1306 " -0.444 2.00e-02 2.50e+03 pdb=" C4' UTP A1306 " 0.351 2.00e-02 2.50e+03 pdb=" C5' UTP A1306 " -0.157 2.00e-02 2.50e+03 pdb=" N1 UTP A1306 " -0.352 2.00e-02 2.50e+03 pdb=" O2' UTP A1306 " 0.240 2.00e-02 2.50e+03 pdb=" O3' UTP A1306 " -0.004 2.00e-02 2.50e+03 pdb=" O4' UTP A1306 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A2M A1304 " -0.570 2.00e-02 2.50e+03 2.24e-01 1.38e+03 pdb=" N9 A2M A1304 " 0.173 2.00e-02 2.50e+03 pdb=" C8 A2M A1304 " 0.267 2.00e-02 2.50e+03 pdb=" N7 A2M A1304 " 0.126 2.00e-02 2.50e+03 pdb=" C5 A2M A1304 " 0.067 2.00e-02 2.50e+03 pdb=" C6 A2M A1304 " -0.082 2.00e-02 2.50e+03 pdb=" N6 A2M A1304 " -0.195 2.00e-02 2.50e+03 pdb=" N1 A2M A1304 " -0.103 2.00e-02 2.50e+03 pdb=" C2 A2M A1304 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A2M A1304 " 0.140 2.00e-02 2.50e+03 pdb=" C4 A2M A1304 " 0.174 2.00e-02 2.50e+03 ... (remaining 11058 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 10 2.06 - 2.77: 12190 2.77 - 3.48: 80496 3.48 - 4.19: 145167 4.19 - 4.90: 248277 Nonbonded interactions: 486140 Sorted by model distance: nonbonded pdb=" OH TYR A1083 " pdb=" O3' U t 5 " model vdw 1.345 2.440 nonbonded pdb=" NE2 HIS A1084 " pdb=" O3B 3PO p 1 " model vdw 1.596 2.520 nonbonded pdb=" OH TYR A1083 " pdb=" C3' U t 5 " model vdw 1.701 3.470 nonbonded pdb=" O2 U t 1 " pdb=" OP2 U t 2 " model vdw 1.767 3.040 nonbonded pdb=" O ASN A1082 " pdb=" CD1 TYR A1083 " model vdw 1.900 3.340 ... (remaining 486135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 135 through 778 or resid 787 through 1333)) selection = (chain 'D' and resid 135 through 1333) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 135 through 1333) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.410 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 129.910 Find NCS groups from input model: 4.280 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.453 62651 Z= 0.603 Angle : 1.218 46.711 85237 Z= 0.676 Chirality : 0.073 1.980 9752 Planarity : 0.010 0.484 11061 Dihedral : 11.590 154.848 23165 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.33 % Favored : 93.34 % Rotamer: Outliers : 1.25 % Allowed : 4.28 % Favored : 94.47 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.38 % Twisted Proline : 0.85 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.07), residues: 7697 helix: -4.32 (0.04), residues: 2730 sheet: -2.70 (0.14), residues: 984 loop : -2.51 (0.08), residues: 3983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP G 543 HIS 0.029 0.002 HIS A 648 PHE 0.058 0.003 PHE B 159 TYR 0.033 0.003 TYR A 870 ARG 0.024 0.001 ARG A 946 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2691 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 2607 time to evaluate : 5.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 28 residues processed: 2652 average time/residue: 0.6135 time to fit residues: 2698.6395 Evaluate side-chains 1707 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1679 time to evaluate : 5.168 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.4827 time to fit residues: 31.8555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 0.6980 chunk 582 optimal weight: 7.9990 chunk 323 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 602 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 366 optimal weight: 6.9990 chunk 448 optimal weight: 3.9990 chunk 698 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 97 GLN A 114 ASN A 126 HIS A 274 GLN A 312 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 586 ASN A 617 GLN A 648 HIS ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A 939 GLN A1020 HIS ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 230 ASN B 346 ASN B 459 GLN C 122 ASN C 156 GLN C 292 ASN ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN C 533 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 GLN C 821 ASN C 942 HIS ** C 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 GLN D 346 HIS D 430 ASN D 661 ASN D 715 ASN D 821 ASN D 933 ASN D 954 GLN D1015 GLN D1112 ASN E 284 ASN E 291 HIS E 292 ASN E 319 GLN E 346 HIS ** E 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 HIS E 690 GLN ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 854 GLN E 867 ASN E 937 ASN E 988 GLN E1112 ASN E1234 GLN F 346 HIS F 407 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 HIS F 561 ASN F 584 HIS F 802 GLN ** F 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 913 ASN F1112 ASN ** F1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1234 GLN F1332 ASN G 124 GLN G 319 GLN G 346 HIS G 430 ASN G 452 ASN G 640 GLN G 942 HIS ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1112 ASN G1121 HIS G1248 HIS Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 62651 Z= 0.249 Angle : 0.727 20.952 85237 Z= 0.368 Chirality : 0.046 0.363 9752 Planarity : 0.006 0.084 11061 Dihedral : 7.676 166.195 8675 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % Rotamer: Outliers : 3.94 % Allowed : 14.67 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.08), residues: 7697 helix: -3.03 (0.07), residues: 2751 sheet: -2.32 (0.15), residues: 950 loop : -2.02 (0.09), residues: 3996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 445 HIS 0.012 0.001 HIS F 407 PHE 0.026 0.002 PHE B 159 TYR 0.032 0.002 TYR A1083 ARG 0.019 0.001 ARG D 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2123 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1858 time to evaluate : 5.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 152 residues processed: 2014 average time/residue: 0.5567 time to fit residues: 1939.3943 Evaluate side-chains 1649 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1497 time to evaluate : 5.167 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 152 outliers final: 1 residues processed: 152 average time/residue: 0.4764 time to fit residues: 145.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 581 optimal weight: 5.9990 chunk 475 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 699 optimal weight: 8.9990 chunk 755 optimal weight: 0.4980 chunk 623 optimal weight: 30.0000 chunk 693 optimal weight: 20.0000 chunk 238 optimal weight: 3.9990 chunk 561 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN B 165 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 320 GLN C 428 GLN C 456 ASN C 572 ASN C 640 GLN C 864 HIS C 942 HIS ** C 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS C1248 HIS C1321 ASN D 293 ASN D 748 GLN D 933 ASN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 HIS ** F 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN G 491 ASN G 682 GLN ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1248 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 62651 Z= 0.230 Angle : 0.677 17.507 85237 Z= 0.335 Chirality : 0.045 0.317 9752 Planarity : 0.005 0.078 11061 Dihedral : 7.035 171.221 8675 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 3.58 % Allowed : 17.33 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.09), residues: 7697 helix: -2.01 (0.08), residues: 2765 sheet: -2.19 (0.15), residues: 981 loop : -1.68 (0.09), residues: 3951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 445 HIS 0.011 0.001 HIS E1203 PHE 0.022 0.002 PHE F 727 TYR 0.032 0.002 TYR A 81 ARG 0.029 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1928 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1687 time to evaluate : 5.304 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 outliers start: 241 outliers final: 121 residues processed: 1819 average time/residue: 0.5558 time to fit residues: 1749.1162 Evaluate side-chains 1561 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1440 time to evaluate : 5.269 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 121 outliers final: 1 residues processed: 121 average time/residue: 0.4462 time to fit residues: 109.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 0.0270 chunk 525 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 333 optimal weight: 0.9980 chunk 469 optimal weight: 0.9990 chunk 702 optimal weight: 0.9990 chunk 743 optimal weight: 0.9980 chunk 366 optimal weight: 20.0000 chunk 665 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 414 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN C 456 ASN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN C 802 GLN C 942 HIS ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN D 479 HIS ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 284 ASN E 369 ASN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN F 452 ASN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 981 HIS G1121 HIS G1248 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.127 62651 Z= 0.151 Angle : 0.630 17.182 85237 Z= 0.308 Chirality : 0.043 0.232 9752 Planarity : 0.004 0.072 11061 Dihedral : 6.700 173.559 8675 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.47 % Allowed : 19.25 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.09), residues: 7697 helix: -1.41 (0.09), residues: 2714 sheet: -1.98 (0.15), residues: 982 loop : -1.54 (0.09), residues: 4001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 445 HIS 0.007 0.001 HIS C 352 PHE 0.023 0.001 PHE A1086 TYR 0.023 0.001 TYR D 548 ARG 0.007 0.000 ARG F1051 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1610 time to evaluate : 5.191 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 outliers start: 166 outliers final: 87 residues processed: 1694 average time/residue: 0.5462 time to fit residues: 1611.5925 Evaluate side-chains 1513 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1426 time to evaluate : 5.206 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 87 outliers final: 1 residues processed: 87 average time/residue: 0.4504 time to fit residues: 80.9938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 3.9990 chunk 421 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 553 optimal weight: 8.9990 chunk 306 optimal weight: 0.4980 chunk 634 optimal weight: 0.6980 chunk 513 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 379 optimal weight: 10.0000 chunk 667 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS A1192 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 414 ASN B 470 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 693 ASN C 698 HIS C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN D1154 ASN D1234 GLN E 293 ASN E 405 HIS ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 283 ASN F 428 GLN ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1234 GLN G1248 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 62651 Z= 0.229 Angle : 0.659 17.542 85237 Z= 0.323 Chirality : 0.044 0.218 9752 Planarity : 0.004 0.084 11061 Dihedral : 6.516 177.913 8675 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 3.34 % Allowed : 19.49 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.09), residues: 7697 helix: -0.94 (0.10), residues: 2742 sheet: -1.85 (0.15), residues: 993 loop : -1.34 (0.10), residues: 3962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 742 HIS 0.023 0.001 HIS D 698 PHE 0.024 0.002 PHE A 627 TYR 0.024 0.002 TYR A 845 ARG 0.009 0.001 ARG D 527 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1663 time to evaluate : 5.331 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: 225 outliers final: 135 residues processed: 1765 average time/residue: 0.5665 time to fit residues: 1735.5139 Evaluate side-chains 1580 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1445 time to evaluate : 5.242 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 135 outliers final: 1 residues processed: 135 average time/residue: 0.4479 time to fit residues: 122.4521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 20.0000 chunk 669 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 436 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 744 optimal weight: 0.9980 chunk 617 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 390 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 134 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 414 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1329 ASN D 173 GLN ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 933 ASN D1015 GLN E 148 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1329 ASN F 243 GLN F 428 GLN ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F1115 ASN ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 62651 Z= 0.263 Angle : 0.669 17.295 85237 Z= 0.328 Chirality : 0.045 0.352 9752 Planarity : 0.004 0.076 11061 Dihedral : 6.451 178.661 8675 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 2.12 % Allowed : 21.83 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.09), residues: 7697 helix: -0.72 (0.10), residues: 2746 sheet: -1.82 (0.15), residues: 1005 loop : -1.25 (0.10), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 260 HIS 0.012 0.001 HIS A 134 PHE 0.025 0.002 PHE D 957 TYR 0.022 0.001 TYR A 845 ARG 0.011 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1602 time to evaluate : 6.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 80 residues processed: 1669 average time/residue: 0.5835 time to fit residues: 1690.9292 Evaluate side-chains 1523 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1443 time to evaluate : 5.250 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 80 outliers final: 1 residues processed: 80 average time/residue: 0.4670 time to fit residues: 77.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 423 optimal weight: 8.9990 chunk 543 optimal weight: 20.0000 chunk 420 optimal weight: 20.0000 chunk 626 optimal weight: 0.5980 chunk 415 optimal weight: 0.6980 chunk 741 optimal weight: 2.9990 chunk 463 optimal weight: 20.0000 chunk 451 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 346 ASN B 459 GLN B 466 HIS ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 690 GLN C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 ASN ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN E 195 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN F 382 HIS ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 769 GLN ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 62651 Z= 0.198 Angle : 0.645 17.166 85237 Z= 0.314 Chirality : 0.044 0.362 9752 Planarity : 0.004 0.075 11061 Dihedral : 6.387 177.618 8675 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 1.51 % Allowed : 23.54 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.09), residues: 7697 helix: -0.52 (0.10), residues: 2740 sheet: -1.71 (0.16), residues: 1000 loop : -1.18 (0.10), residues: 3957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 445 HIS 0.013 0.001 HIS A 364 PHE 0.018 0.001 PHE B 159 TYR 0.027 0.001 TYR C1031 ARG 0.013 0.000 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1561 time to evaluate : 5.319 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 outliers start: 102 outliers final: 61 residues processed: 1596 average time/residue: 0.5650 time to fit residues: 1558.2409 Evaluate side-chains 1499 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1438 time to evaluate : 5.294 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4764 time to fit residues: 62.4898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 442 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 471 optimal weight: 0.4980 chunk 504 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 582 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 632 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 414 ASN B 466 HIS ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1321 ASN D1329 ASN E 148 GLN E 195 ASN E 283 ASN E 284 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS ** E1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 291 HIS F 382 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 62651 Z= 0.281 Angle : 0.695 17.324 85237 Z= 0.338 Chirality : 0.046 0.532 9752 Planarity : 0.004 0.077 11061 Dihedral : 6.414 156.977 8675 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 1.86 % Allowed : 24.19 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.10), residues: 7697 helix: -0.47 (0.10), residues: 2751 sheet: -1.74 (0.15), residues: 999 loop : -1.14 (0.10), residues: 3947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F1164 HIS 0.030 0.001 HIS A1084 PHE 0.039 0.002 PHE C 727 TYR 0.021 0.002 TYR C1031 ARG 0.015 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1530 time to evaluate : 5.348 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: 125 outliers final: 88 residues processed: 1579 average time/residue: 0.6031 time to fit residues: 1655.3120 Evaluate side-chains 1490 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1402 time to evaluate : 5.234 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.4870 time to fit residues: 88.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 0.3980 chunk 710 optimal weight: 4.9990 chunk 647 optimal weight: 30.0000 chunk 690 optimal weight: 10.0000 chunk 709 optimal weight: 1.9990 chunk 415 optimal weight: 0.8980 chunk 300 optimal weight: 0.3980 chunk 542 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 624 optimal weight: 20.0000 chunk 653 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN B 9 HIS B 212 ASN B 466 HIS C 291 HIS ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 942 HIS ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 GLN D1321 ASN D1329 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 ASN F 382 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1186 GLN F1205 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1321 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62651 Z= 0.162 Angle : 0.668 17.154 85237 Z= 0.323 Chirality : 0.044 0.332 9752 Planarity : 0.004 0.073 11061 Dihedral : 6.299 158.604 8675 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 0.62 % Allowed : 25.93 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 7697 helix: -0.27 (0.10), residues: 2744 sheet: -1.64 (0.16), residues: 976 loop : -1.08 (0.10), residues: 3977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 742 HIS 0.026 0.001 HIS A1084 PHE 0.027 0.001 PHE D 449 TYR 0.027 0.001 TYR C 170 ARG 0.013 0.000 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1529 time to evaluate : 5.371 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: 42 outliers final: 26 residues processed: 1545 average time/residue: 0.5728 time to fit residues: 1531.2273 Evaluate side-chains 1433 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1407 time to evaluate : 5.252 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4887 time to fit residues: 30.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 9.9990 chunk 453 optimal weight: 1.9990 chunk 730 optimal weight: 0.9990 chunk 445 optimal weight: 5.9990 chunk 346 optimal weight: 0.9990 chunk 507 optimal weight: 9.9990 chunk 766 optimal weight: 3.9990 chunk 705 optimal weight: 6.9990 chunk 610 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 471 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN B 9 HIS B 527 GLN C 284 ASN ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN C 942 HIS ** C1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 GLN D 718 ASN D 769 GLN D1329 ASN E 148 GLN E 195 ASN ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS E1234 GLN F 382 HIS F 438 ASN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1295 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62651 Z= 0.169 Angle : 0.665 17.159 85237 Z= 0.321 Chirality : 0.044 0.540 9752 Planarity : 0.004 0.065 11061 Dihedral : 6.222 162.285 8675 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 0.50 % Allowed : 27.27 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7697 helix: -0.15 (0.10), residues: 2727 sheet: -1.58 (0.16), residues: 967 loop : -1.03 (0.10), residues: 4003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 742 HIS 0.024 0.001 HIS A 364 PHE 0.042 0.001 PHE C 727 TYR 0.032 0.001 TYR F1101 ARG 0.014 0.000 ARG E1051 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15394 Ramachandran restraints generated. 7697 Oldfield, 0 Emsley, 7697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1475 time to evaluate : 5.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 1483 average time/residue: 0.5894 time to fit residues: 1522.5641 Evaluate side-chains 1423 residues out of total 6733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1400 time to evaluate : 5.285 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5056 time to fit residues: 28.6630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 649 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 562 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 611 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 627 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 412 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 414 ASN B 466 HIS C 284 ASN ** C 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 HIS C 942 HIS C1016 ASN ** C1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 GLN D1329 ASN E 156 GLN E 284 ASN E 293 ASN E 711 ASN ** E 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 639 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108035 restraints weight = 103476.272| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.46 r_work: 0.3210 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 62651 Z= 0.253 Angle : 0.694 17.233 85237 Z= 0.337 Chirality : 0.046 0.416 9752 Planarity : 0.004 0.071 11061 Dihedral : 6.280 160.766 8675 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 0.71 % Allowed : 27.48 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.39 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 7697 helix: -0.12 (0.10), residues: 2726 sheet: -1.70 (0.15), residues: 999 loop : -1.02 (0.10), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1042 HIS 0.023 0.001 HIS A 364 PHE 0.043 0.002 PHE C 727 TYR 0.025 0.001 TYR A 845 ARG 0.014 0.001 ARG F 441 =============================================================================== Job complete usr+sys time: 23864.04 seconds wall clock time: 413 minutes 59.88 seconds (24839.88 seconds total)