Starting phenix.real_space_refine on Wed Nov 20 06:38:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/11_2024/7ozo_13130.cif" } resolution = 3.8 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= -0.001 sd= 0.935 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: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 312 5.16 5 C 34364 2.51 5 N 9406 2.21 5 O 10238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54330 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17106 SG CYS C 88 110.833 62.048 14.810 1.00 88.38 S ATOM 17119 SG CYS C 90 107.907 64.011 13.282 1.00 96.15 S ATOM 17154 SG CYS C 94 108.066 60.694 12.146 1.00 91.04 S ATOM 17176 SG CYS C 97 107.328 60.749 15.562 1.00 91.66 S ATOM 24473 SG CYS I 17 24.539 43.044 99.997 1.00113.62 S ATOM 24497 SG CYS I 20 23.294 46.096 98.277 1.00113.40 S ATOM 24658 SG CYS I 39 25.806 46.385 101.253 1.00119.61 S ATOM 24683 SG CYS I 42 22.186 45.472 101.832 1.00115.46 S ATOM 25035 SG CYS I 86 50.252 11.048 87.504 1.00 96.86 S ATOM 25059 SG CYS I 89 47.588 9.306 85.327 1.00 99.62 S ATOM 25263 SG CYS I 114 49.977 12.014 83.864 1.00 90.30 S ATOM 25298 SG CYS I 119 47.163 12.872 86.198 1.00 98.27 S ATOM 25408 SG CYS J 7 95.886 38.182 35.465 1.00 53.15 S ATOM 25432 SG CYS J 10 99.443 37.196 34.354 1.00 45.28 S ATOM 25696 SG CYS J 44 97.689 35.363 37.208 1.00 44.27 S ATOM 25702 SG CYS J 45 96.612 34.900 33.595 1.00 47.53 S ATOM 26830 SG CYS L 19 61.149 60.757 19.647 1.00121.75 S ATOM 26849 SG CYS L 22 61.352 59.542 16.086 1.00128.01 S ATOM 26966 SG CYS L 36 59.632 62.873 16.914 1.00126.33 S ATOM 26992 SG CYS L 39 57.972 59.565 17.710 1.00128.84 S Restraints were copied for chains: U, T, V, S, M, P, O, W, N, X, Q, R Time building chain proxies: 46.60, per 1000 atoms: 0.86 Number of scatterers: 54330 At special positions: 0 Unit cell: (159.315, 218.139, 148.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 312 16.00 O 10238 8.00 N 9406 7.00 C 34364 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 - 3.00 Amino acid : True - 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: 12.19 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 90 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 97 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 88 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 17 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 42 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 20 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 39 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 119 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 114 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 89 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 86 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 22 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 36 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 39 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 19 " Number of angles added : 60 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12796 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 78 sheets defined 39.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.811A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.635A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.660A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.679A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.061A pdb=" N ASP A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.563A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.878A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.556A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 removed outlier: 3.509A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.722A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.975A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.517A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.585A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 3.523A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1281 through 1293 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.927A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.746A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 4.038A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.290A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.524A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.574A pdb=" N ARG B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.661A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.558A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.143A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.700A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.612A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.548A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.159A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.512A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.693A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.568A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.861A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.999A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.961A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.685A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.900A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.555A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.351A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.240A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.523A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 removed outlier: 3.653A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.776A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.701A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.160A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.427A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 4.084A pdb=" N GLU D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.910A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.636A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.583A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.599A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.813A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.607A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.971A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.633A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.275A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 4.114A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.797A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.642A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.773A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.190A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.849A pdb=" N LYS K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 395 through 397 No H-bonds generated for 'chain 'M' and resid 395 through 397' Processing helix chain 'M' and resid 398 through 409 removed outlier: 3.810A pdb=" N GLY M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 508 through 519 Processing helix chain 'M' and resid 520 through 525 Processing helix chain 'M' and resid 538 through 549 removed outlier: 3.635A pdb=" N THR M 543 " --> pdb=" O GLN M 539 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA M 544 " --> pdb=" O ASP M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 556 through 566 removed outlier: 3.661A pdb=" N ASN M 562 " --> pdb=" O GLY M 558 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 566 " --> pdb=" O ASN M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 596 removed outlier: 3.678A pdb=" N LEU M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE M 595 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 616 removed outlier: 4.062A pdb=" N ASP M 614 " --> pdb=" O PRO M 610 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 660 Processing helix chain 'M' and resid 661 through 684 removed outlier: 3.563A pdb=" N THR M 665 " --> pdb=" O GLY M 661 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE M 682 " --> pdb=" O ASN M 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 688 through 693 removed outlier: 3.879A pdb=" N SER M 692 " --> pdb=" O GLY M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 695 through 722 Processing helix chain 'M' and resid 732 through 760 Processing helix chain 'M' and resid 764 through 773 Processing helix chain 'M' and resid 777 through 785 Processing helix chain 'M' and resid 832 through 869 removed outlier: 3.557A pdb=" N PHE M 837 " --> pdb=" O PRO M 833 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA M 855 " --> pdb=" O ALA M 851 " (cutoff:3.500A) Processing helix chain 'M' and resid 890 through 894 Processing helix chain 'M' and resid 914 through 921 removed outlier: 3.509A pdb=" N LYS M 918 " --> pdb=" O LYS M 914 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 934 Processing helix chain 'M' and resid 935 through 945 removed outlier: 3.723A pdb=" N ASN M 945 " --> pdb=" O ASP M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 970 removed outlier: 3.974A pdb=" N GLN M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG M 967 " --> pdb=" O ARG M 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 968 " --> pdb=" O GLU M 964 " (cutoff:3.500A) Processing helix chain 'M' and resid 982 through 994 Processing helix chain 'M' and resid 1005 through 1020 removed outlier: 3.518A pdb=" N VAL M1009 " --> pdb=" O HIS M1005 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL M1010 " --> pdb=" O PRO M1006 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M1018 " --> pdb=" O LYS M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1027 through 1038 Processing helix chain 'M' and resid 1038 through 1049 Processing helix chain 'M' and resid 1050 through 1057 Processing helix chain 'M' and resid 1061 through 1080 Processing helix chain 'M' and resid 1086 through 1100 Proline residue: M1098 - end of helix Processing helix chain 'M' and resid 1120 through 1129 Processing helix chain 'M' and resid 1145 through 1149 Processing helix chain 'M' and resid 1151 through 1153 No H-bonds generated for 'chain 'M' and resid 1151 through 1153' Processing helix chain 'M' and resid 1154 through 1162 Processing helix chain 'M' and resid 1165 through 1169 removed outlier: 3.586A pdb=" N VAL M1169 " --> pdb=" O THR M1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1165 through 1169' Processing helix chain 'M' and resid 1189 through 1199 removed outlier: 3.523A pdb=" N ASN M1194 " --> pdb=" O GLN M1190 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL M1195 " --> pdb=" O GLU M1191 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET M1199 " --> pdb=" O VAL M1195 " (cutoff:3.500A) Processing helix chain 'M' and resid 1217 through 1225 Processing helix chain 'M' and resid 1227 through 1240 Processing helix chain 'M' and resid 1262 through 1267 Processing helix chain 'M' and resid 1281 through 1293 Processing helix chain 'M' and resid 1342 through 1348 removed outlier: 3.928A pdb=" N SER M1348 " --> pdb=" O MET M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1361 through 1369 Processing helix chain 'M' and resid 1370 through 1389 removed outlier: 3.747A pdb=" N LYS M1376 " --> pdb=" O GLU M1372 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP M1389 " --> pdb=" O VAL M1385 " (cutoff:3.500A) Processing helix chain 'M' and resid 1394 through 1406 Processing helix chain 'M' and resid 1478 through 1482 removed outlier: 4.037A pdb=" N TYR M1482 " --> pdb=" O LYS M1479 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 4.290A pdb=" N GLN N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU N 24 " --> pdb=" O ASP N 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 53 removed outlier: 3.524A pdb=" N SER N 46 " --> pdb=" O GLN N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 61 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.573A pdb=" N ARG N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 174 Processing helix chain 'N' and resid 248 through 253 Processing helix chain 'N' and resid 269 through 277 Processing helix chain 'N' and resid 280 through 289 removed outlier: 3.660A pdb=" N ILE N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 310 removed outlier: 4.168A pdb=" N MET N 298 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Proline residue: N 303 - end of helix removed outlier: 3.558A pdb=" N ASP N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL N 310 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 removed outlier: 4.143A pdb=" N ARG N 324 " --> pdb=" O PHE N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 3.702A pdb=" N ARG N 335 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE N 336 " --> pdb=" O LYS N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 378 Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 395 through 426 removed outlier: 3.612A pdb=" N GLY N 406 " --> pdb=" O PHE N 402 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET N 407 " --> pdb=" O LEU N 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS N 421 " --> pdb=" O ILE N 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE N 422 " --> pdb=" O TYR N 418 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG N 425 " --> pdb=" O LYS N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 removed outlier: 3.547A pdb=" N ALA N 434 " --> pdb=" O ASN N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 451 removed outlier: 4.159A pdb=" N ILE N 440 " --> pdb=" O LYS N 436 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 444 " --> pdb=" O ILE N 440 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 447 " --> pdb=" O GLY N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 483 Processing helix chain 'N' and resid 490 through 496 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.512A pdb=" N LEU N 505 " --> pdb=" O HIS N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 548 removed outlier: 3.692A pdb=" N GLU N 546 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP N 548 " --> pdb=" O PHE N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 562 removed outlier: 3.568A pdb=" N ALA N 562 " --> pdb=" O ALA N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 593 removed outlier: 3.861A pdb=" N LEU N 583 " --> pdb=" O ASP N 579 " (cutoff:3.500A) Processing helix chain 'N' and resid 607 through 609 No H-bonds generated for 'chain 'N' and resid 607 through 609' Processing helix chain 'N' and resid 636 through 645 Processing helix chain 'N' and resid 652 through 659 removed outlier: 3.997A pdb=" N LEU N 656 " --> pdb=" O SER N 652 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL N 657 " --> pdb=" O TRP N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 672 removed outlier: 3.961A pdb=" N THR N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 678 through 684 removed outlier: 3.684A pdb=" N LEU N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU N 684 " --> pdb=" O ASP N 680 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 704 Processing helix chain 'N' and resid 705 through 710 removed outlier: 3.900A pdb=" N ILE N 710 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 718 through 732 removed outlier: 3.555A pdb=" N ALA N 727 " --> pdb=" O THR N 723 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS N 730 " --> pdb=" O SER N 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 762 through 767 removed outlier: 4.350A pdb=" N TYR N 766 " --> pdb=" O ARG N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 803 Processing helix chain 'N' and resid 969 through 972 Processing helix chain 'N' and resid 977 through 994 removed outlier: 4.240A pdb=" N LEU N 981 " --> pdb=" O THR N 977 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1017 removed outlier: 3.523A pdb=" N ASP N1017 " --> pdb=" O ASN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1054 through 1061 removed outlier: 3.652A pdb=" N LYS N1058 " --> pdb=" O MET N1054 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 40 removed outlier: 3.776A pdb=" N ILE O 39 " --> pdb=" O ARG O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 removed outlier: 3.701A pdb=" N LEU O 68 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU O 70 " --> pdb=" O HIS O 66 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE O 71 " --> pdb=" O ARG O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 118 through 120 No H-bonds generated for 'chain 'O' and resid 118 through 120' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 240 through 271 removed outlier: 4.159A pdb=" N VAL O 245 " --> pdb=" O PRO O 241 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU O 246 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 removed outlier: 4.427A pdb=" N THR P 28 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 29' Processing helix chain 'P' and resid 33 through 51 Processing helix chain 'P' and resid 58 through 71 Processing helix chain 'P' and resid 76 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 115 Processing helix chain 'P' and resid 115 through 122 removed outlier: 4.083A pdb=" N GLU P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY P 120 " --> pdb=" O PRO P 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG P 121 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.911A pdb=" N ASP P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 removed outlier: 3.637A pdb=" N TYR Q 8 " --> pdb=" O GLU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.583A pdb=" N LEU Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Q 34 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 34' Processing helix chain 'Q' and resid 36 through 45 removed outlier: 3.598A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 98 removed outlier: 3.813A pdb=" N GLU Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 121 removed outlier: 3.614A pdb=" N GLN Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 136 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 58 through 75 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 21 through 34 removed outlier: 3.971A pdb=" N THR S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 32 " --> pdb=" O GLN S 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 75 removed outlier: 3.634A pdb=" N SER U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 4.276A pdb=" N ASP U 106 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 26 removed outlier: 4.114A pdb=" N GLU V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 39 removed outlier: 3.796A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 51 removed outlier: 3.642A pdb=" N MET V 48 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.773A pdb=" N SER W 9 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.190A pdb=" N ILE W 45 " --> pdb=" O THR W 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN W 49 " --> pdb=" O ILE W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 68 Processing helix chain 'W' and resid 82 through 115 removed outlier: 3.849A pdb=" N LYS W 110 " --> pdb=" O ARG W 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.124A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.520A pdb=" N CYS A 602 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AA8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.917A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1320 through 1322 removed outlier: 3.757A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.613A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.532A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.735A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.500A pdb=" N PHE B 208 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 233 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC2, first strand: chain 'B' and resid 572 through 573 removed outlier: 5.969A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC6, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.980A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 827 through 828 removed outlier: 4.814A pdb=" N CYS B 837 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 891 " --> pdb=" O CYS B 837 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 839 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.625A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.771A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.882A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD4, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.247A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.065A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.871A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 92 removed outlier: 7.305A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AD9, first strand: chain 'H' and resid 101 through 102 removed outlier: 4.189A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE3, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AE4, first strand: chain 'M' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR M 368 " --> pdb=" O LEU M 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL M 378 " --> pdb=" O ARG M 475 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU M 477 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL M 380 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 389 through 393 removed outlier: 4.125A pdb=" N TYR M 418 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS M 449 " --> pdb=" O ALA M 416 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA M 416 " --> pdb=" O HIS M 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 554 through 555 Processing sheet with id=AE7, first strand: chain 'M' and resid 602 through 605 removed outlier: 3.518A pdb=" N CYS M 602 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL M 629 " --> pdb=" O ILE M 636 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 789 through 790 Processing sheet with id=AE9, first strand: chain 'M' and resid 872 through 873 Processing sheet with id=AF1, first strand: chain 'M' and resid 902 through 905 Processing sheet with id=AF2, first strand: chain 'M' and resid 1307 through 1310 removed outlier: 3.917A pdb=" N ILE M1335 " --> pdb=" O HIS M1310 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR M1358 " --> pdb=" O THR M1140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU M1255 " --> pdb=" O LEU M1216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN M1172 " --> pdb=" O GLU M1215 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR U 54 " --> pdb=" O ILE M1175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 1320 through 1322 removed outlier: 3.757A pdb=" N LYS M1329 " --> pdb=" O ILE M1321 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY S 57 " --> pdb=" O LEU M1475 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU M1473 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE S 54 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS S 71 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE S 75 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL S 48 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE S 77 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE S 46 " --> pdb=" O PHE S 77 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 65 through 67 removed outlier: 3.614A pdb=" N TYR N 84 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR N 84 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE N 133 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU N 86 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR N 131 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE N 88 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR N 129 " --> pdb=" O PHE N 88 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN N 90 " --> pdb=" O ASP N 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL N 126 " --> pdb=" O PHE N 148 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE N 148 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE N 128 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS N 146 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS N 130 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS N 144 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL N 132 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR N 142 " --> pdb=" O VAL N 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.532A pdb=" N SER N 106 " --> pdb=" O HIS N 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 185 through 187 Processing sheet with id=AG1, first strand: chain 'N' and resid 391 through 394 removed outlier: 3.735A pdb=" N ALA N 196 " --> pdb=" O ARG N 484 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 206 through 209 removed outlier: 3.532A pdb=" N TYR N 217 " --> pdb=" O MET N 239 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE N 235 " --> pdb=" O CYS N 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER N 233 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP N 236 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG4, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG5, first strand: chain 'N' and resid 572 through 573 removed outlier: 5.969A pdb=" N LYS N 566 " --> pdb=" O ILE N 612 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE N 614 " --> pdb=" O LYS N 566 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE N 568 " --> pdb=" O ILE N 614 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL N 907 " --> pdb=" O LYS X 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 759 through 760 Processing sheet with id=AG9, first strand: chain 'N' and resid 1025 through 1026 removed outlier: 6.981A pdb=" N VAL N 794 " --> pdb=" O GLY N 946 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN N 948 " --> pdb=" O VAL N 794 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET N 796 " --> pdb=" O GLN N 948 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE N 965 " --> pdb=" O ILE N 779 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 967 " --> pdb=" O ALA N 781 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE N1042 " --> pdb=" O ILE N 782 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 827 through 828 removed outlier: 4.815A pdb=" N CYS N 837 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP N 891 " --> pdb=" O CYS N 837 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY N 839 " --> pdb=" O ASP N 891 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 865 through 867 removed outlier: 3.625A pdb=" N ILE N 866 " --> pdb=" O THR N 894 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR N 894 " --> pdb=" O ILE N 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 956 through 957 Processing sheet with id=AH4, first strand: chain 'O' and resid 8 through 14 removed outlier: 6.772A pdb=" N LYS O 20 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU O 14 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASN O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN O 232 " --> pdb=" O VAL O 182 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL O 182 " --> pdb=" O ASN O 232 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU O 234 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 121 through 122 removed outlier: 6.883A pdb=" N GLU O 158 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN O 55 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG O 160 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS O 166 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE O 47 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY O 168 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE O 45 " --> pdb=" O GLY O 168 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 113 through 116 Processing sheet with id=AH7, first strand: chain 'Q' and resid 26 through 27 removed outlier: 4.247A pdb=" N ALA Q 63 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL Q 60 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Q 62 " --> pdb=" O MET Q 72 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG Q 101 " --> pdb=" O GLN Q 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Q 128 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 81 through 82 removed outlier: 4.066A pdb=" N VAL Q 82 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 147 through 151 removed outlier: 3.873A pdb=" N GLU Q 147 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL Q 190 " --> pdb=" O MET Q 151 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 83 through 92 removed outlier: 7.306A pdb=" N PHE S 98 " --> pdb=" O THR S 90 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER S 105 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA S 159 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER S 162 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE S 147 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU S 83 " --> pdb=" O ILE S 147 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 117 through 118 Processing sheet with id=AI3, first strand: chain 'T' and resid 101 through 102 removed outlier: 4.190A pdb=" N ARG T 111 " --> pdb=" O ASP T 102 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU T 122 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU T 41 " --> pdb=" O LEU T 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU T 31 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL T 12 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE T 60 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU T 7 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU T 58 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE T 9 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE T 56 " --> pdb=" O ILE T 9 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL T 96 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER T 117 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG T 98 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 26 through 28 Processing sheet with id=AI5, first strand: chain 'U' and resid 80 through 81 Processing sheet with id=AI6, first strand: chain 'W' and resid 21 through 23 2235 hydrogen bonds defined for protein. 6285 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: 28.34 Time building geometry restraints manager: 14.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 18152 1.35 - 1.46: 11834 1.46 - 1.58: 24870 1.58 - 1.70: 0 1.70 - 1.82: 496 Bond restraints: 55352 Sorted by residual: bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 55347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 73242 1.03 - 2.06: 1151 2.06 - 3.09: 174 3.09 - 4.13: 215 4.13 - 5.16: 4 Bond angle restraints: 74786 Sorted by residual: angle pdb=" C ILE B 972 " pdb=" CA ILE B 972 " pdb=" CB ILE B 972 " ideal model delta sigma weight residual 113.70 110.55 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" C ILE N 972 " pdb=" CA ILE N 972 " pdb=" CB ILE N 972 " ideal model delta sigma weight residual 113.70 110.57 3.13 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C ALA B 971 " pdb=" N ILE B 972 " pdb=" CA ILE B 972 " ideal model delta sigma weight residual 120.43 123.23 -2.80 9.60e-01 1.09e+00 8.48e+00 angle pdb=" C ALA N 971 " pdb=" N ILE N 972 " pdb=" CA ILE N 972 " ideal model delta sigma weight residual 120.43 123.16 -2.73 9.60e-01 1.09e+00 8.11e+00 angle pdb=" C ASN N 227 " pdb=" CA ASN N 227 " pdb=" CB ASN N 227 " ideal model delta sigma weight residual 110.42 114.61 -4.19 1.99e+00 2.53e-01 4.44e+00 ... (remaining 74781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 30773 17.89 - 35.78: 2522 35.78 - 53.67: 447 53.67 - 71.57: 102 71.57 - 89.46: 76 Dihedral angle restraints: 33920 sinusoidal: 14154 harmonic: 19766 Sorted by residual: dihedral pdb=" CA GLU B 226 " pdb=" C GLU B 226 " pdb=" N ASN B 227 " pdb=" CA ASN B 227 " ideal model delta harmonic sigma weight residual -180.00 -135.94 -44.06 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA GLU N 226 " pdb=" C GLU N 226 " pdb=" N ASN N 227 " pdb=" CA ASN N 227 " ideal model delta harmonic sigma weight residual 180.00 -135.97 -44.03 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA CYS O 90 " pdb=" C CYS O 90 " pdb=" N GLU O 91 " pdb=" CA GLU O 91 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 33917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5813 0.030 - 0.060: 1531 0.060 - 0.090: 437 0.090 - 0.120: 524 0.120 - 0.150: 57 Chirality restraints: 8362 Sorted by residual: chirality pdb=" CA ILE M 596 " pdb=" N ILE M 596 " pdb=" C ILE M 596 " pdb=" CB ILE M 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE V 3 " pdb=" N ILE V 3 " pdb=" C ILE V 3 " pdb=" CB ILE V 3 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE A 798 " pdb=" N ILE A 798 " pdb=" C ILE A 798 " pdb=" CB ILE A 798 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 8359 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 395 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO M 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO M 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 521 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 522 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " -0.020 5.00e-02 4.00e+02 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 510 2.57 - 3.16: 46299 3.16 - 3.74: 85542 3.74 - 4.32: 120471 4.32 - 4.90: 200227 Nonbonded interactions: 453049 Sorted by model distance: nonbonded pdb=" OD1 ASN M 372 " pdb=" OH TYR N 788 " model vdw 1.993 3.040 nonbonded pdb=" OD1 ASN A 372 " pdb=" OH TYR B 788 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR A 763 " pdb=" OD2 ASP H 23 " model vdw 2.019 3.040 nonbonded pdb=" OH TYR M 763 " pdb=" OD2 ASP T 23 " model vdw 2.020 3.040 nonbonded pdb=" OG SER M 867 " pdb=" OG1 THR M1415 " model vdw 2.075 3.040 ... (remaining 453044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 2.120 Check model and map are aligned: 0.380 Set scattering table: 0.500 Process input model: 144.820 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 : 0.002 0.034 55352 Z= 0.113 Angle : 0.385 5.156 74786 Z= 0.212 Chirality : 0.039 0.150 8362 Planarity : 0.002 0.058 9702 Dihedral : 14.069 89.457 21124 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.21 (0.11), residues: 6690 helix: 2.06 (0.12), residues: 2164 sheet: 0.25 (0.17), residues: 974 loop : 0.26 (0.11), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 453 HIS 0.003 0.000 HIS B 518 PHE 0.007 0.000 PHE Q 44 TYR 0.018 0.001 TYR X 41 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1802 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1802 time to evaluate : 6.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 VAL cc_start: 0.9098 (t) cc_final: 0.8876 (t) REVERT: A 635 LEU cc_start: 0.8949 (tp) cc_final: 0.8639 (tt) REVERT: A 668 PHE cc_start: 0.8281 (t80) cc_final: 0.7802 (t80) REVERT: A 804 HIS cc_start: 0.6386 (m-70) cc_final: 0.5937 (m170) REVERT: A 1086 MET cc_start: 0.6177 (mmt) cc_final: 0.5195 (pmm) REVERT: A 1158 LEU cc_start: 0.8339 (tt) cc_final: 0.7891 (tt) REVERT: A 1168 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8333 (tttp) REVERT: A 1371 ILE cc_start: 0.5956 (tp) cc_final: 0.5729 (tp) REVERT: B 550 MET cc_start: 0.8302 (tmm) cc_final: 0.8013 (tmm) REVERT: B 551 GLU cc_start: 0.7019 (pm20) cc_final: 0.6320 (pm20) REVERT: B 584 MET cc_start: 0.7820 (mmm) cc_final: 0.6996 (tmm) REVERT: B 854 ILE cc_start: 0.8028 (tt) cc_final: 0.7827 (mt) REVERT: B 977 THR cc_start: 0.7540 (p) cc_final: 0.6392 (p) REVERT: C 50 VAL cc_start: 0.7169 (t) cc_final: 0.6920 (m) REVERT: D 33 LEU cc_start: 0.6583 (mt) cc_final: 0.5763 (mp) REVERT: D 34 ASN cc_start: 0.7470 (m-40) cc_final: 0.6280 (t0) REVERT: D 80 ILE cc_start: 0.8569 (mt) cc_final: 0.8216 (tp) REVERT: G 17 TYR cc_start: 0.8119 (m-80) cc_final: 0.7435 (m-10) REVERT: G 45 VAL cc_start: 0.8078 (t) cc_final: 0.7727 (m) REVERT: G 164 MET cc_start: 0.5319 (mmm) cc_final: 0.5107 (tpt) REVERT: I 34 ILE cc_start: 0.8696 (tp) cc_final: 0.8293 (tp) REVERT: I 44 TYR cc_start: 0.7541 (t80) cc_final: 0.6321 (t80) REVERT: I 75 ASP cc_start: 0.7128 (t0) cc_final: 0.6852 (t0) REVERT: J 24 LEU cc_start: 0.7329 (mt) cc_final: 0.7025 (mp) REVERT: J 25 LEU cc_start: 0.6843 (mt) cc_final: 0.6521 (mt) REVERT: K 95 ILE cc_start: 0.7928 (mm) cc_final: 0.7653 (mm) REVERT: M 804 HIS cc_start: 0.6729 (m-70) cc_final: 0.6387 (m90) REVERT: M 1086 MET cc_start: 0.6333 (mmt) cc_final: 0.5496 (pmm) REVERT: M 1158 LEU cc_start: 0.8358 (tt) cc_final: 0.7904 (tt) REVERT: M 1168 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8526 (tttp) REVERT: M 1234 LYS cc_start: 0.8321 (tmtt) cc_final: 0.7404 (tptm) REVERT: N 30 ILE cc_start: 0.8338 (mt) cc_final: 0.8006 (mt) REVERT: N 118 LEU cc_start: 0.8170 (pp) cc_final: 0.7312 (mt) REVERT: N 550 MET cc_start: 0.8252 (tmm) cc_final: 0.7902 (tmm) REVERT: N 584 MET cc_start: 0.7862 (mmm) cc_final: 0.6971 (tmm) REVERT: N 725 GLN cc_start: 0.8025 (tp40) cc_final: 0.7811 (tp40) REVERT: N 766 TYR cc_start: 0.7143 (m-80) cc_final: 0.6758 (m-10) REVERT: N 977 THR cc_start: 0.7505 (p) cc_final: 0.7300 (p) REVERT: O 50 VAL cc_start: 0.6983 (t) cc_final: 0.6669 (m) REVERT: O 149 LEU cc_start: 0.8189 (pt) cc_final: 0.7909 (tt) REVERT: P 33 LEU cc_start: 0.6651 (mt) cc_final: 0.5697 (mp) REVERT: P 34 ASN cc_start: 0.7476 (m-40) cc_final: 0.6390 (t0) REVERT: P 80 ILE cc_start: 0.8431 (mt) cc_final: 0.8103 (tp) REVERT: Q 177 ASP cc_start: 0.6833 (t70) cc_final: 0.6587 (t70) REVERT: S 17 TYR cc_start: 0.8137 (m-80) cc_final: 0.7613 (m-10) REVERT: S 24 ASN cc_start: 0.7566 (t0) cc_final: 0.6712 (t0) REVERT: S 45 VAL cc_start: 0.8283 (t) cc_final: 0.7972 (m) REVERT: T 48 TYR cc_start: 0.7266 (t80) cc_final: 0.7031 (t80) REVERT: U 34 ILE cc_start: 0.8591 (tp) cc_final: 0.8168 (tp) REVERT: U 44 TYR cc_start: 0.7534 (t80) cc_final: 0.6345 (t80) REVERT: U 75 ASP cc_start: 0.7089 (t0) cc_final: 0.6695 (t0) REVERT: V 24 LEU cc_start: 0.6912 (mt) cc_final: 0.6409 (mp) REVERT: W 95 ILE cc_start: 0.7725 (mm) cc_final: 0.7489 (mm) outliers start: 0 outliers final: 0 residues processed: 1802 average time/residue: 0.7571 time to fit residues: 2226.2901 Evaluate side-chains 866 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 6.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 9.9990 chunk 503 optimal weight: 0.0870 chunk 279 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 520 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 602 optimal weight: 0.8980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 410 ASN A 780 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN A1194 ASN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B 631 GLN ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN C 32 ASN C 265 HIS ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN I 22 ASN I 60 HIS I 84 HIS I 118 HIS ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN K 49 GLN L 23 HIS M 410 ASN M 485 ASN M 504 HIS ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1194 ASN ** M1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** N 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN N 631 GLN ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN O 51 GLN O 177 ASN O 265 HIS ** Q 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 HIS U 84 HIS U 118 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN W 49 GLN X 23 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55352 Z= 0.292 Angle : 0.676 10.397 74786 Z= 0.352 Chirality : 0.047 0.164 8362 Planarity : 0.005 0.063 9702 Dihedral : 3.775 54.299 7396 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.81 % Allowed : 11.99 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 6690 helix: 1.05 (0.11), residues: 2320 sheet: -0.05 (0.16), residues: 1000 loop : 0.04 (0.11), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 479 HIS 0.014 0.002 HIS I 84 PHE 0.029 0.002 PHE B1042 TYR 0.028 0.002 TYR X 41 ARG 0.011 0.001 ARG U 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 961 time to evaluate : 6.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8344 (ppp) cc_final: 0.7825 (ptt) REVERT: A 803 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7757 (mtpt) REVERT: A 1086 MET cc_start: 0.6490 (mmt) cc_final: 0.5716 (pmm) REVERT: A 1130 ILE cc_start: 0.6486 (mm) cc_final: 0.6000 (mm) REVERT: A 1142 PHE cc_start: 0.7634 (m-80) cc_final: 0.7389 (m-80) REVERT: A 1168 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8249 (ttmt) REVERT: A 1221 MET cc_start: 0.7037 (mtp) cc_final: 0.6672 (mtp) REVERT: A 1356 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7329 (ttp-110) REVERT: B 147 THR cc_start: 0.7559 (m) cc_final: 0.7227 (p) REVERT: B 550 MET cc_start: 0.7945 (tmm) cc_final: 0.7582 (tmm) REVERT: B 725 GLN cc_start: 0.8377 (tp40) cc_final: 0.8038 (tp-100) REVERT: B 766 TYR cc_start: 0.7582 (m-10) cc_final: 0.7150 (m-10) REVERT: D 33 LEU cc_start: 0.6402 (mt) cc_final: 0.5643 (mp) REVERT: D 34 ASN cc_start: 0.7009 (m-40) cc_final: 0.6502 (t0) REVERT: D 44 ARG cc_start: 0.7328 (tpt170) cc_final: 0.6819 (tpm170) REVERT: D 70 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6999 (ttt180) REVERT: D 80 ILE cc_start: 0.8487 (mt) cc_final: 0.8272 (tp) REVERT: D 112 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8151 (mmmm) REVERT: D 142 TYR cc_start: 0.4927 (t80) cc_final: 0.4322 (t80) REVERT: E 130 PHE cc_start: 0.7182 (m-80) cc_final: 0.6873 (m-80) REVERT: E 137 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7644 (tp) REVERT: F 123 LEU cc_start: 0.7704 (mt) cc_final: 0.7313 (mt) REVERT: H 57 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7708 (tmm-80) REVERT: I 75 ASP cc_start: 0.7882 (t0) cc_final: 0.7584 (t0) REVERT: K 45 ILE cc_start: 0.8378 (mm) cc_final: 0.7941 (mt) REVERT: K 68 GLU cc_start: 0.6773 (tp30) cc_final: 0.6563 (tp30) REVERT: M 501 MET cc_start: 0.8448 (ppp) cc_final: 0.7962 (ptt) REVERT: M 804 HIS cc_start: 0.6790 (m-70) cc_final: 0.6403 (m-70) REVERT: M 1086 MET cc_start: 0.6517 (mmt) cc_final: 0.6052 (pmm) REVERT: M 1234 LYS cc_start: 0.8536 (tmtt) cc_final: 0.7903 (tptm) REVERT: M 1293 LEU cc_start: 0.8671 (mp) cc_final: 0.8216 (mt) REVERT: M 1296 MET cc_start: 0.5964 (mmm) cc_final: 0.4190 (mmm) REVERT: N 513 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7590 (mt-10) REVERT: N 725 GLN cc_start: 0.8505 (tp40) cc_final: 0.8204 (tp40) REVERT: O 26 THR cc_start: 0.5866 (m) cc_final: 0.5650 (m) REVERT: O 45 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8377 (tp) REVERT: O 149 LEU cc_start: 0.8326 (pt) cc_final: 0.7934 (tt) REVERT: P 33 LEU cc_start: 0.6486 (mt) cc_final: 0.5735 (mp) REVERT: P 34 ASN cc_start: 0.7035 (m-40) cc_final: 0.6642 (t0) REVERT: P 39 MET cc_start: 0.7414 (tmm) cc_final: 0.7117 (tmm) REVERT: P 62 MET cc_start: 0.6752 (mmp) cc_final: 0.6489 (mmp) REVERT: Q 37 LEU cc_start: 0.8337 (tp) cc_final: 0.8123 (tp) REVERT: Q 110 MET cc_start: 0.7337 (tpp) cc_final: 0.7019 (tpt) REVERT: R 101 LYS cc_start: 0.8239 (mmmm) cc_final: 0.8032 (mmmm) REVERT: R 123 LEU cc_start: 0.7734 (mt) cc_final: 0.7160 (mt) REVERT: S 117 MET cc_start: 0.4627 (mmm) cc_final: 0.3814 (mmm) REVERT: S 146 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7658 (mmmt) REVERT: T 5 LEU cc_start: 0.8027 (mp) cc_final: 0.7773 (tp) REVERT: T 28 LEU cc_start: 0.6713 (pt) cc_final: 0.5974 (mp) REVERT: T 48 TYR cc_start: 0.7529 (t80) cc_final: 0.7159 (t80) REVERT: U 46 GLN cc_start: 0.7321 (pm20) cc_final: 0.6739 (pm20) REVERT: U 75 ASP cc_start: 0.7761 (t0) cc_final: 0.7450 (t0) REVERT: W 24 ASP cc_start: 0.7046 (t0) cc_final: 0.6604 (t0) outliers start: 169 outliers final: 90 residues processed: 1074 average time/residue: 0.6571 time to fit residues: 1180.8154 Evaluate side-chains 805 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 713 time to evaluate : 6.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 49 GLN Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 508 SER Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 614 ASP Chi-restraints excluded: chain M residue 663 ASP Chi-restraints excluded: chain M residue 746 ASN Chi-restraints excluded: chain M residue 754 SER Chi-restraints excluded: chain M residue 1121 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 373 LEU Chi-restraints excluded: chain N residue 453 TRP Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 682 LEU Chi-restraints excluded: chain N residue 778 SER Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 91 ILE Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain X residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 501 optimal weight: 6.9990 chunk 410 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 604 optimal weight: 10.0000 chunk 652 optimal weight: 0.8980 chunk 537 optimal weight: 4.9990 chunk 599 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN B 52 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 19 GLN D 47 GLN E 132 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 673 GLN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1263 ASN ** N 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN N 699 HIS N 930 GLN ** Q 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55352 Z= 0.223 Angle : 0.620 9.165 74786 Z= 0.317 Chirality : 0.045 0.185 8362 Planarity : 0.004 0.065 9702 Dihedral : 3.910 60.753 7396 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 14.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 6690 helix: 0.99 (0.11), residues: 2332 sheet: -0.20 (0.15), residues: 1066 loop : -0.10 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 49 HIS 0.016 0.001 HIS P 43 PHE 0.022 0.002 PHE B1042 TYR 0.045 0.002 TYR E 26 ARG 0.018 0.001 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 819 time to evaluate : 6.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8452 (ppp) cc_final: 0.8084 (ptt) REVERT: A 668 PHE cc_start: 0.8443 (t80) cc_final: 0.7946 (t80) REVERT: A 735 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: A 803 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7716 (mtpt) REVERT: A 1086 MET cc_start: 0.6510 (mmt) cc_final: 0.5783 (pmm) REVERT: B 262 TYR cc_start: 0.7127 (m-10) cc_final: 0.6908 (m-10) REVERT: B 531 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6792 (p90) REVERT: B 550 MET cc_start: 0.7968 (tmm) cc_final: 0.6542 (tmm) REVERT: B 744 MET cc_start: 0.8125 (mmt) cc_final: 0.7921 (mmm) REVERT: C 50 VAL cc_start: 0.7430 (t) cc_final: 0.7183 (m) REVERT: C 262 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: D 19 GLN cc_start: 0.6100 (mp10) cc_final: 0.5732 (mp10) REVERT: D 33 LEU cc_start: 0.6315 (mt) cc_final: 0.5847 (mp) REVERT: D 34 ASN cc_start: 0.7052 (m-40) cc_final: 0.6728 (m-40) REVERT: D 80 ILE cc_start: 0.8446 (mt) cc_final: 0.8229 (tt) REVERT: D 112 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8289 (mmmm) REVERT: F 61 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: F 96 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7955 (mt-10) REVERT: G 164 MET cc_start: 0.5413 (mmm) cc_final: 0.4270 (tpt) REVERT: I 75 ASP cc_start: 0.7911 (t0) cc_final: 0.7629 (t0) REVERT: K 45 ILE cc_start: 0.8318 (mm) cc_final: 0.7879 (mt) REVERT: M 501 MET cc_start: 0.8426 (ppp) cc_final: 0.8197 (ptt) REVERT: M 804 HIS cc_start: 0.6785 (m-70) cc_final: 0.6512 (m90) REVERT: M 863 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7376 (mtp180) REVERT: M 903 PHE cc_start: 0.7834 (m-80) cc_final: 0.7465 (m-80) REVERT: M 1086 MET cc_start: 0.6417 (mmt) cc_final: 0.5960 (pmm) REVERT: M 1234 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8106 (tptm) REVERT: M 1296 MET cc_start: 0.6017 (mmm) cc_final: 0.5040 (mmm) REVERT: N 30 ILE cc_start: 0.8525 (mt) cc_final: 0.8273 (mm) REVERT: N 471 ASN cc_start: 0.7235 (t0) cc_final: 0.6991 (m110) REVERT: N 513 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7570 (mt-10) REVERT: N 531 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6645 (p90) REVERT: N 550 MET cc_start: 0.7913 (tmm) cc_final: 0.7599 (tmm) REVERT: N 584 MET cc_start: 0.7803 (mmm) cc_final: 0.7577 (mmm) REVERT: N 840 MET cc_start: 0.6323 (mpp) cc_final: 0.6080 (mmt) REVERT: O 149 LEU cc_start: 0.8278 (pt) cc_final: 0.8018 (tt) REVERT: O 262 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: P 34 ASN cc_start: 0.7130 (m-40) cc_final: 0.6891 (m-40) REVERT: P 70 ARG cc_start: 0.7089 (ttt180) cc_final: 0.6463 (tpp80) REVERT: Q 37 LEU cc_start: 0.8417 (tp) cc_final: 0.8139 (tp) REVERT: Q 177 ASP cc_start: 0.7101 (t70) cc_final: 0.6754 (t70) REVERT: R 96 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7977 (mt-10) REVERT: R 123 LEU cc_start: 0.7572 (mt) cc_final: 0.7202 (mt) REVERT: S 146 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7618 (mmmt) REVERT: T 5 LEU cc_start: 0.8005 (mp) cc_final: 0.7715 (tp) REVERT: T 42 ASP cc_start: 0.6666 (m-30) cc_final: 0.6428 (m-30) REVERT: T 48 TYR cc_start: 0.7498 (t80) cc_final: 0.7127 (t80) REVERT: T 65 TYR cc_start: 0.5725 (m-10) cc_final: 0.5146 (m-10) REVERT: U 37 TYR cc_start: 0.5654 (m-10) cc_final: 0.5437 (m-10) REVERT: U 75 ASP cc_start: 0.7751 (t0) cc_final: 0.7413 (t0) REVERT: W 33 PHE cc_start: 0.8596 (m-80) cc_final: 0.8255 (m-10) outliers start: 172 outliers final: 94 residues processed: 927 average time/residue: 0.6564 time to fit residues: 1025.7017 Evaluate side-chains 784 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 684 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 508 SER Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 614 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 663 ASP Chi-restraints excluded: chain M residue 746 ASN Chi-restraints excluded: chain M residue 754 SER Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 972 THR Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1362 ILE Chi-restraints excluded: chain M residue 1415 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 356 PHE Chi-restraints excluded: chain N residue 453 TRP Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 682 LEU Chi-restraints excluded: chain N residue 761 THR Chi-restraints excluded: chain N residue 778 SER Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 130 PHE Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 95 ILE Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain X residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 0.9980 chunk 454 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 405 optimal weight: 2.9990 chunk 606 optimal weight: 0.4980 chunk 641 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 chunk 574 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 52 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 38 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1101 GLN ** N 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 725 GLN O 6 GLN P 38 HIS ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 GLN ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55352 Z= 0.242 Angle : 0.614 10.237 74786 Z= 0.314 Chirality : 0.045 0.329 8362 Planarity : 0.004 0.066 9702 Dihedral : 4.079 69.443 7396 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.45 % Allowed : 15.89 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 6690 helix: 0.88 (0.11), residues: 2350 sheet: -0.35 (0.15), residues: 1082 loop : -0.16 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 11 HIS 0.011 0.001 HIS P 43 PHE 0.030 0.002 PHE N 769 TYR 0.030 0.002 TYR L 41 ARG 0.010 0.001 ARG X 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 6024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 752 time to evaluate : 6.520 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: A 501 MET cc_start: 0.8448 (ppp) cc_final: 0.8133 (ptt) REVERT: A 668 PHE cc_start: 0.8402 (t80) cc_final: 0.7913 (t80) REVERT: A 735 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: A 803 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7762 (mtpt) REVERT: A 1085 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 1086 MET cc_start: 0.6485 (mmt) cc_final: 0.5853 (pmm) REVERT: B 368 MET cc_start: 0.8373 (mtm) cc_final: 0.8115 (ttp) REVERT: B 471 ASN cc_start: 0.7213 (t0) cc_final: 0.6830 (m-40) REVERT: B 655 ASP cc_start: 0.6100 (m-30) cc_final: 0.5841 (m-30) REVERT: B 840 MET cc_start: 0.6101 (mpp) cc_final: 0.5878 (mmt) REVERT: C 50 VAL cc_start: 0.7490 (t) cc_final: 0.7245 (m) REVERT: D 16 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7118 (t70) REVERT: D 19 GLN cc_start: 0.6135 (mp10) cc_final: 0.5722 (mp10) REVERT: D 33 LEU cc_start: 0.6513 (mt) cc_final: 0.6131 (mp) REVERT: D 34 ASN cc_start: 0.7152 (m-40) cc_final: 0.6831 (m-40) REVERT: D 70 ARG cc_start: 0.7393 (ttt180) cc_final: 0.6613 (tpp80) REVERT: F 61 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5717 (mt-10) REVERT: F 96 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7978 (mt-10) REVERT: F 123 LEU cc_start: 0.7583 (mt) cc_final: 0.7328 (mt) REVERT: H 96 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8321 (t) REVERT: I 75 ASP cc_start: 0.7941 (t0) cc_final: 0.------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 508 SER Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 545 VAL Chi-restraints excluded: chain M residue 614 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 663 ASP Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain M residue 692 SER Chi-restraints excluded: chain M residue 754 SER Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1362 ILE Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain M residue 1404 THR Chi-restraints excluded: chain M residue 1415 THR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 220 GLU Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 356 PHE Chi-restraints excluded: chain N residue 368 MET Chi-restraints excluded: chain N residue 453 TRP Chi-restraints excluded: chain N residue 466 VAL Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 682 LEU Chi-restraints excluded: chain N residue 760 THR Chi-restraints excluded: chain N residue 761 THR Chi-restraints excluded: chain N residue 778 SER Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 939 HIS Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 104 ASP Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 130 PHE Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 87 PHE Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 95 ILE Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain X residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 477 optimal weight: 4.9990 chunk 264 optimal weight: 0.0670 chunk 547 optimal weight: 10.0000 chunk 443 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 576 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: