Starting phenix.real_space_refine on Sun Apr 14 08:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap9_11851/04_2024/7ap9_11851_neut.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 19801 2.51 5 N 5138 2.21 5 O 5784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A PHE 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1263": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B GLU 931": "OE1" <-> "OE2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B ARG 1047": "NH1" <-> "NH2" Residue "B ARG 1058": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "I TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 583": "NH1" <-> "NH2" Residue "I ARG 595": "NH1" <-> "NH2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30881 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3903 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 443} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "S" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 952 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 89.098 103.263 61.297 1.00133.50 S ATOM 382 SG CYS A 52 92.766 103.153 60.361 1.00126.58 S ATOM 434 SG CYS A 59 91.093 100.167 62.119 1.00122.37 S ATOM 694 SG CYS A 90 75.503 100.632 108.162 1.00155.92 S ATOM 718 SG CYS A 93 77.134 103.838 109.373 1.00162.06 S ATOM 1016 SG CYS A 130 76.679 101.014 111.747 1.00161.58 S ATOM 1059 SG CYS A 135 73.631 102.857 110.714 1.00165.37 S ATOM 18688 SG CYS B1087 99.216 104.479 75.606 1.00109.10 S ATOM 18711 SG CYS B1090 95.658 103.225 76.196 1.00111.20 S ATOM 18800 SG CYS B1103 96.127 105.787 73.776 1.00111.30 S ATOM 18825 SG CYS B1106 96.658 106.724 77.394 1.00115.40 S ATOM 27059 SG CYS I 326 101.651 96.021 37.377 1.00214.92 S ATOM 27372 SG CYS I 363 99.819 92.714 38.389 1.00191.93 S ATOM 27396 SG CYS I 366 103.225 93.533 39.896 1.00189.01 S Time building chain proxies: 17.73, per 1000 atoms: 0.57 Number of scatterers: 30881 At special positions: 0 Unit cell: (162.716, 152.081, 153.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 142 16.00 P 11 15.00 Mg 1 11.99 O 5784 8.00 N 5138 7.00 C 19801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.95 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 48 sheets defined 42.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.604A pdb=" N LYS A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.637A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 6.156A pdb=" N LYS A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.726A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.753A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.245A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.552A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.917A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.719A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.720A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.605A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.704A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.193A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.526A pdb=" N VAL A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.375A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1170 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.603A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.650A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.512A pdb=" N ASN B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.846A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.621A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.523A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.606A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 391 removed outlier: 3.636A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.570A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.079A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.580A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.636A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.792A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.617A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.834A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.689A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 924 removed outlier: 4.389A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.138A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.516A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1021 through 1026 removed outlier: 3.620A pdb=" N LYS B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.659A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 4.082A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.313A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.735A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.914A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.520A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.521A pdb=" N ARG C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.736A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.581A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 4.043A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.792A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 5.940A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.704A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.883A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.141A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.523A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.490A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.602A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.560A pdb=" N VAL J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 Processing helix chain 'S' and resid 72 through 81 Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.572A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.385A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.222A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.863A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.441A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.505A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.516A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB2, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB3, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB4, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB5, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.837A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.837A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.653A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE B 98 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU B 121 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.653A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.984A pdb=" N VAL B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.712A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.441A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.811A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.835A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.835A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD2, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.497A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 996 through 997 removed outlier: 3.683A pdb=" N LYS B1002 " --> pdb=" O ASP B 997 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.552A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AE1, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.461A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.221A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 90 removed outlier: 4.420A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE7, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.315A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.384A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AF1, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AF2, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AF3, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.192A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3651 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: 14.41 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9820 1.34 - 1.46: 7445 1.46 - 1.59: 14021 1.59 - 1.71: 20 1.71 - 1.83: 223 Bond restraints: 31529 Sorted by residual: bond pdb=" C ARG B 347 " pdb=" N TYR B 348 " ideal model delta sigma weight residual 1.331 1.234 0.097 3.12e-02 1.03e+03 9.71e+00 bond pdb=" C ILE B 909 " pdb=" N THR B 910 " ideal model delta sigma weight residual 1.331 1.272 0.059 2.07e-02 2.33e+03 8.25e+00 bond pdb=" C GLU B 719 " pdb=" N ARG B 720 " ideal model delta sigma weight residual 1.330 1.306 0.024 1.47e-02 4.63e+03 2.62e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.45e+00 bond pdb=" N GLU A 461 " pdb=" CA GLU A 461 " ideal model delta sigma weight residual 1.458 1.438 0.019 1.30e-02 5.92e+03 2.20e+00 ... (remaining 31524 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.56: 553 105.56 - 112.68: 16894 112.68 - 119.80: 10853 119.80 - 126.92: 14055 126.92 - 134.04: 307 Bond angle restraints: 42662 Sorted by residual: angle pdb=" N VAL B 401 " pdb=" CA VAL B 401 " pdb=" C VAL B 401 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.63e+00 angle pdb=" C TYR B 467 " pdb=" N LEU B 468 " pdb=" CA LEU B 468 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.45e+00 angle pdb=" C GLU S 69 " pdb=" N SER S 70 " pdb=" CA SER S 70 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.10e+00 angle pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " pdb=" CG PHE A 938 " ideal model delta sigma weight residual 113.80 116.78 -2.98 1.00e+00 1.00e+00 8.89e+00 ... (remaining 42657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 17806 17.26 - 34.51: 1053 34.51 - 51.77: 214 51.77 - 69.03: 51 69.03 - 86.28: 11 Dihedral angle restraints: 19135 sinusoidal: 7941 harmonic: 11194 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -162.14 76.14 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA VAL I 660 " pdb=" C VAL I 660 " pdb=" N HIS I 661 " pdb=" CA HIS I 661 " ideal model delta harmonic sigma weight residual -180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 19132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2761 0.035 - 0.071: 1460 0.071 - 0.106: 412 0.106 - 0.141: 186 0.141 - 0.176: 10 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CA PHE A 938 " pdb=" N PHE A 938 " pdb=" C PHE A 938 " pdb=" CB PHE A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE I 222 " pdb=" N ILE I 222 " pdb=" C ILE I 222 " pdb=" CB ILE I 222 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 4826 not shown) Planarity restraints: 5361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 856 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ARG B 856 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG B 856 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 857 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.020 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE A 938 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 35 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C TYR B 35 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR B 35 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 36 " 0.012 2.00e-02 2.50e+03 ... (remaining 5358 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 395 2.60 - 3.17: 28526 3.17 - 3.75: 46198 3.75 - 4.32: 69204 4.32 - 4.90: 114528 Nonbonded interactions: 258851 Sorted by model distance: nonbonded pdb=" OG1 THR B 303 " pdb=" O ASN B 305 " model vdw 2.023 2.440 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.028 2.440 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.041 2.170 nonbonded pdb=" OH TYR B 512 " pdb=" OD2 ASP B 551 " model vdw 2.064 2.440 nonbonded pdb=" O LYS B 60 " pdb=" OG1 THR B 63 " model vdw 2.079 2.440 ... (remaining 258846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.270 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 88.940 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: