Starting phenix.real_space_refine on Fri Dec 8 10:52:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpg_14120/12_2023/7qpg_14120_neut.pdb" } resolution = 3.9 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= 0.004 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 298 5.16 5 C 36562 2.51 5 N 9506 2.21 5 O 10798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 263": "OD1" <-> "OD2" Residue "R PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 1004": "OE1" <-> "OE2" Residue "R GLU 1065": "OE1" <-> "OE2" Residue "R GLU 1163": "OE1" <-> "OE2" Residue "R PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 263": "OD1" <-> "OD2" Residue "S PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 1004": "OE1" <-> "OE2" Residue "S GLU 1065": "OE1" <-> "OE2" Residue "S GLU 1163": "OE1" <-> "OE2" Residue "S PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 128": "OE1" <-> "OE2" Residue "W PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 236": "OE1" <-> "OE2" Residue "W GLU 372": "OE1" <-> "OE2" Residue "W PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 769": "OE1" <-> "OE2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 236": "OE1" <-> "OE2" Residue "X GLU 372": "OE1" <-> "OE2" Residue "X PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 769": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 57164 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4737 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 563} Chain: "C" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4737 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 563} Chain: "R" Number of atoms: 17614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2208, 17614 Classifications: {'peptide': 2208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 69, 'TRANS': 2134} Chain: "S" Number of atoms: 17614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2208, 17614 Classifications: {'peptide': 2208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 69, 'TRANS': 2134} Chain: "W" Number of atoms: 6231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6231 Classifications: {'peptide': 779} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 747} Chain: "X" Number of atoms: 6231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6231 Classifications: {'peptide': 779} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 747} Time building chain proxies: 21.03, per 1000 atoms: 0.37 Number of scatterers: 57164 At special positions: 0 Unit cell: (189, 491.4, 160.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 298 16.00 O 10798 8.00 N 9506 7.00 C 36562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.45 Conformation dependent library (CDL) restraints added in 7.7 seconds 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13812 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 20 sheets defined 63.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.206A pdb=" N ALA B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.674A pdb=" N HIS B 193 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.815A pdb=" N GLU B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 311 Processing helix chain 'B' and resid 328 through 340 removed outlier: 4.151A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 362 through 380 removed outlier: 4.087A pdb=" N LEU B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 367 " --> pdb=" O TYR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.811A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.764A pdb=" N ILE B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 4.356A pdb=" N TYR B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 482 removed outlier: 3.544A pdb=" N CYS B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Proline residue: B 479 - end of helix Processing helix chain 'B' and resid 484 through 502 removed outlier: 3.585A pdb=" N LEU B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.896A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 removed outlier: 4.207A pdb=" N ALA C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.674A pdb=" N HIS C 193 " --> pdb=" O HIS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 282 removed outlier: 3.814A pdb=" N GLU C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 Processing helix chain 'C' and resid 328 through 340 removed outlier: 4.151A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 340 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'C' and resid 362 through 380 removed outlier: 4.086A pdb=" N LEU C 366 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 367 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.811A pdb=" N LYS C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.764A pdb=" N ILE C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 removed outlier: 4.354A pdb=" N TYR C 449 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 482 removed outlier: 3.545A pdb=" N CYS C 477 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 484 through 502 removed outlier: 3.584A pdb=" N LEU C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.895A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 16 removed outlier: 3.655A pdb=" N THR R 13 " --> pdb=" O ASN R 10 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY R 14 " --> pdb=" O ASP R 11 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER R 15 " --> pdb=" O ASP R 12 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY R 16 " --> pdb=" O THR R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 178 Processing helix chain 'R' and resid 180 through 189 Processing helix chain 'R' and resid 398 through 406 removed outlier: 4.118A pdb=" N ARG R 402 " --> pdb=" O ASN R 398 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS R 406 " --> pdb=" O ARG R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 408 through 420 removed outlier: 3.775A pdb=" N SER R 414 " --> pdb=" O ALA R 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 440 Processing helix chain 'R' and resid 447 through 465 removed outlier: 3.620A pdb=" N TRP R 451 " --> pdb=" O GLU R 447 " (cutoff:3.500A) Processing helix chain 'R' and resid 467 through 477 Processing helix chain 'R' and resid 482 through 501 Processing helix chain 'R' and resid 509 through 530 removed outlier: 3.733A pdb=" N THR R 523 " --> pdb=" O HIS R 519 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR R 524 " --> pdb=" O ALA R 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR R 526 " --> pdb=" O LEU R 522 " (cutoff:3.500A) Processing helix chain 'R' and resid 535 through 545 Processing helix chain 'R' and resid 547 through 559 removed outlier: 4.406A pdb=" N ASP R 551 " --> pdb=" O ASP R 547 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE R 552 " --> pdb=" O ASP R 548 " (cutoff:3.500A) Processing helix chain 'R' and resid 560 through 571 Processing helix chain 'R' and resid 575 through 579 Processing helix chain 'R' and resid 580 through 591 Processing helix chain 'R' and resid 600 through 607 Processing helix chain 'R' and resid 607 through 616 Processing helix chain 'R' and resid 619 through 638 removed outlier: 3.703A pdb=" N ARG R 632 " --> pdb=" O GLU R 628 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU R 635 " --> pdb=" O ALA R 631 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU R 636 " --> pdb=" O ARG R 632 " (cutoff:3.500A) Processing helix chain 'R' and resid 643 through 651 Processing helix chain 'R' and resid 667 through 671 removed outlier: 3.733A pdb=" N ILE R 671 " --> pdb=" O TRP R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 679 through 701 Processing helix chain 'R' and resid 707 through 712 Processing helix chain 'R' and resid 715 through 726 Processing helix chain 'R' and resid 729 through 731 No H-bonds generated for 'chain 'R' and resid 729 through 731' Processing helix chain 'R' and resid 732 through 740 Processing helix chain 'R' and resid 740 through 747 Processing helix chain 'R' and resid 752 through 769 removed outlier: 3.528A pdb=" N SER R 769 " --> pdb=" O ASN R 765 " (cutoff:3.500A) Processing helix chain 'R' and resid 777 through 790 removed outlier: 3.693A pdb=" N ALA R 781 " --> pdb=" O THR R 777 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA R 785 " --> pdb=" O ALA R 781 " (cutoff:3.500A) Processing helix chain 'R' and resid 793 through 805 removed outlier: 3.545A pdb=" N PHE R 797 " --> pdb=" O THR R 793 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP R 798 " --> pdb=" O ASP R 794 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA R 799 " --> pdb=" O LEU R 795 " (cutoff:3.500A) Processing helix chain 'R' and resid 812 through 825 removed outlier: 3.661A pdb=" N GLU R 824 " --> pdb=" O LYS R 820 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET R 825 " --> pdb=" O GLN R 821 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 849 Processing helix chain 'R' and resid 860 through 870 Processing helix chain 'R' and resid 875 through 887 removed outlier: 3.556A pdb=" N VAL R 883 " --> pdb=" O ASP R 879 " (cutoff:3.500A) Processing helix chain 'R' and resid 890 through 905 removed outlier: 4.259A pdb=" N ILE R 894 " --> pdb=" O SER R 890 " (cutoff:3.500A) Processing helix chain 'R' and resid 907 through 918 Processing helix chain 'R' and resid 919 through 940 removed outlier: 3.687A pdb=" N LYS R 925 " --> pdb=" O ALA R 921 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU R 940 " --> pdb=" O LEU R 936 " (cutoff:3.500A) Processing helix chain 'R' and resid 945 through 970 removed outlier: 3.897A pdb=" N ASP R 961 " --> pdb=" O LYS R 957 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE R 962 " --> pdb=" O THR R 958 " (cutoff:3.500A) Processing helix chain 'R' and resid 973 through 998 removed outlier: 3.932A pdb=" N GLU R 979 " --> pdb=" O GLN R 975 " (cutoff:3.500A) Processing helix chain 'R' and resid 1002 through 1008 removed outlier: 3.600A pdb=" N ASN R1008 " --> pdb=" O GLU R1004 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1029 removed outlier: 3.838A pdb=" N VAL R1012 " --> pdb=" O ASN R1008 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1060 removed outlier: 3.534A pdb=" N LYS R1051 " --> pdb=" O SER R1047 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA R1058 " --> pdb=" O ARG R1054 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R1059 " --> pdb=" O GLN R1055 " (cutoff:3.500A) Processing helix chain 'R' and resid 1062 through 1077 Processing helix chain 'R' and resid 1080 through 1094 Processing helix chain 'R' and resid 1096 through 1116 Processing helix chain 'R' and resid 1127 through 1142 removed outlier: 3.798A pdb=" N ILE R1142 " --> pdb=" O GLN R1138 " (cutoff:3.500A) Processing helix chain 'R' and resid 1147 through 1167 removed outlier: 3.527A pdb=" N HIS R1157 " --> pdb=" O GLU R1153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET R1160 " --> pdb=" O LYS R1156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN R1167 " --> pdb=" O GLU R1163 " (cutoff:3.500A) Processing helix chain 'R' and resid 1178 through 1183 removed outlier: 4.099A pdb=" N GLY R1182 " --> pdb=" O LYS R1178 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R1183 " --> pdb=" O ALA R1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1178 through 1183' Processing helix chain 'R' and resid 1188 through 1192 removed outlier: 4.338A pdb=" N TRP R1191 " --> pdb=" O TYR R1188 " (cutoff:3.500A) Processing helix chain 'R' and resid 1205 through 1208 removed outlier: 3.731A pdb=" N MET R1208 " --> pdb=" O GLU R1205 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1205 through 1208' Processing helix chain 'R' and resid 1209 through 1221 Processing helix chain 'R' and resid 1247 through 1265 removed outlier: 3.992A pdb=" N VAL R1251 " --> pdb=" O LEU R1247 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN R1261 " --> pdb=" O ALA R1257 " (cutoff:3.500A) Processing helix chain 'R' and resid 1267 through 1288 removed outlier: 3.853A pdb=" N ARG R1273 " --> pdb=" O GLU R1269 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER R1286 " --> pdb=" O CYS R1282 " (cutoff:3.500A) Processing helix chain 'R' and resid 1292 through 1301 removed outlier: 4.381A pdb=" N LYS R1298 " --> pdb=" O THR R1294 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R1299 " --> pdb=" O LEU R1295 " (cutoff:3.500A) Processing helix chain 'R' and resid 1302 through 1336 removed outlier: 3.598A pdb=" N GLU R1325 " --> pdb=" O ILE R1321 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R1329 " --> pdb=" O GLU R1325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE R1335 " --> pdb=" O LEU R1331 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN R1336 " --> pdb=" O HIS R1332 " (cutoff:3.500A) Processing helix chain 'R' and resid 1341 through 1350 removed outlier: 3.614A pdb=" N THR R1350 " --> pdb=" O LEU R1346 " (cutoff:3.500A) Processing helix chain 'R' and resid 1355 through 1367 removed outlier: 4.164A pdb=" N GLU R1359 " --> pdb=" O LYS R1355 " (cutoff:3.500A) Processing helix chain 'R' and resid 1371 through 1389 removed outlier: 3.519A pdb=" N ILE R1375 " --> pdb=" O ASN R1371 " (cutoff:3.500A) Processing helix chain 'R' and resid 1391 through 1414 removed outlier: 3.516A pdb=" N GLY R1395 " --> pdb=" O GLU R1391 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R1396 " --> pdb=" O ILE R1392 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS R1397 " --> pdb=" O GLU R1393 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R1414 " --> pdb=" O ARG R1410 " (cutoff:3.500A) Processing helix chain 'R' and resid 1418 through 1422 removed outlier: 3.837A pdb=" N VAL R1421 " --> pdb=" O PHE R1418 " (cutoff:3.500A) Processing helix chain 'R' and resid 1425 through 1429 Processing helix chain 'R' and resid 1430 through 1438 removed outlier: 4.320A pdb=" N LYS R1434 " --> pdb=" O LYS R1430 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA R1435 " --> pdb=" O ASP R1431 " (cutoff:3.500A) Processing helix chain 'R' and resid 1443 through 1454 removed outlier: 3.518A pdb=" N PHE R1454 " --> pdb=" O TYR R1450 " (cutoff:3.500A) Processing helix chain 'R' and resid 1457 through 1476 removed outlier: 3.675A pdb=" N VAL R1461 " --> pdb=" O ASP R1457 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR R1473 " --> pdb=" O LEU R1469 " (cutoff:3.500A) Processing helix chain 'R' and resid 1482 through 1502 removed outlier: 3.617A pdb=" N SER R1486 " --> pdb=" O ALA R1482 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG R1489 " --> pdb=" O ASP R1485 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG R1490 " --> pdb=" O SER R1486 " (cutoff:3.500A) Proline residue: R1492 - end of helix removed outlier: 3.876A pdb=" N GLU R1500 " --> pdb=" O ALA R1496 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET R1501 " --> pdb=" O LYS R1497 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R1502 " --> pdb=" O ALA R1498 " (cutoff:3.500A) Processing helix chain 'R' and resid 1503 through 1505 No H-bonds generated for 'chain 'R' and resid 1503 through 1505' Processing helix chain 'R' and resid 1508 through 1521 Processing helix chain 'R' and resid 1526 through 1541 Processing helix chain 'R' and resid 1551 through 1562 removed outlier: 3.744A pdb=" N ILE R1555 " --> pdb=" O GLN R1551 " (cutoff:3.500A) Processing helix chain 'R' and resid 1569 through 1579 removed outlier: 3.760A pdb=" N HIS R1579 " --> pdb=" O TYR R1575 " (cutoff:3.500A) Processing helix chain 'R' and resid 1584 through 1589 Processing helix chain 'R' and resid 1600 through 1608 Processing helix chain 'R' and resid 1609 through 1612 removed outlier: 3.853A pdb=" N LEU R1612 " --> pdb=" O SER R1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1609 through 1612' Processing helix chain 'R' and resid 1615 through 1628 removed outlier: 4.592A pdb=" N THR R1619 " --> pdb=" O GLU R1615 " (cutoff:3.500A) Processing helix chain 'R' and resid 1630 through 1646 removed outlier: 4.013A pdb=" N LEU R1634 " --> pdb=" O SER R1630 " (cutoff:3.500A) Processing helix chain 'R' and resid 1646 through 1655 removed outlier: 3.965A pdb=" N LYS R1650 " --> pdb=" O LYS R1646 " (cutoff:3.500A) Processing helix chain 'R' and resid 1660 through 1680 removed outlier: 4.437A pdb=" N LYS R1665 " --> pdb=" O THR R1661 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU R1666 " --> pdb=" O LEU R1662 " (cutoff:3.500A) Processing helix chain 'R' and resid 1683 through 1698 removed outlier: 3.503A pdb=" N ALA R1687 " --> pdb=" O ASN R1683 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER R1693 " --> pdb=" O ALA R1689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP R1697 " --> pdb=" O SER R1693 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R1698 " --> pdb=" O LEU R1694 " (cutoff:3.500A) Processing helix chain 'R' and resid 1701 through 1721 Processing helix chain 'R' and resid 1727 through 1755 removed outlier: 3.534A pdb=" N LYS R1731 " --> pdb=" O GLU R1727 " (cutoff:3.500A) Processing helix chain 'R' and resid 1759 through 1765 Processing helix chain 'R' and resid 1768 through 1777 Processing helix chain 'R' and resid 1779 through 1788 removed outlier: 4.025A pdb=" N ASN R1783 " --> pdb=" O HIS R1779 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE R1786 " --> pdb=" O ILE R1782 " (cutoff:3.500A) Processing helix chain 'R' and resid 1796 through 1809 removed outlier: 3.708A pdb=" N GLU R1803 " --> pdb=" O ALA R1799 " (cutoff:3.500A) Processing helix chain 'R' and resid 1811 through 1825 removed outlier: 4.213A pdb=" N VAL R1815 " --> pdb=" O ASN R1811 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS R1825 " --> pdb=" O GLU R1821 " (cutoff:3.500A) Processing helix chain 'R' and resid 1833 through 1839 removed outlier: 3.579A pdb=" N GLU R1839 " --> pdb=" O SER R1835 " (cutoff:3.500A) Processing helix chain 'R' and resid 1840 through 1842 No H-bonds generated for 'chain 'R' and resid 1840 through 1842' Processing helix chain 'R' and resid 1843 through 1856 removed outlier: 3.664A pdb=" N ARG R1847 " --> pdb=" O ASP R1843 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER R1855 " --> pdb=" O TYR R1851 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG R1856 " --> pdb=" O LEU R1852 " (cutoff:3.500A) Processing helix chain 'R' and resid 1857 through 1871 removed outlier: 3.514A pdb=" N ARG R1863 " --> pdb=" O ASP R1859 " (cutoff:3.500A) Processing helix chain 'R' and resid 1882 through 1897 Processing helix chain 'R' and resid 1898 through 1907 removed outlier: 3.538A pdb=" N LEU R1905 " --> pdb=" O THR R1901 " (cutoff:3.500A) Processing helix chain 'R' and resid 1909 through 1929 Processing helix chain 'R' and resid 1934 through 1938 Processing helix chain 'R' and resid 1942 through 1954 removed outlier: 3.631A pdb=" N MET R1946 " --> pdb=" O PRO R1942 " (cutoff:3.500A) Processing helix chain 'R' and resid 1957 through 1972 removed outlier: 3.728A pdb=" N GLU R1970 " --> pdb=" O GLU R1966 " (cutoff:3.500A) Processing helix chain 'R' and resid 1975 through 1989 removed outlier: 3.553A pdb=" N LEU R1987 " --> pdb=" O LEU R1983 " (cutoff:3.500A) Processing helix chain 'R' and resid 1991 through 2002 Processing helix chain 'R' and resid 2006 through 2011 removed outlier: 3.610A pdb=" N GLN R2010 " --> pdb=" O SER R2007 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R2011 " --> pdb=" O LEU R2008 " (cutoff:3.500A) Processing helix chain 'R' and resid 2013 through 2029 removed outlier: 3.583A pdb=" N ARG R2020 " --> pdb=" O LYS R2016 " (cutoff:3.500A) Proline residue: R2025 - end of helix Processing helix chain 'R' and resid 2034 through 2051 Processing helix chain 'R' and resid 2053 through 2057 Processing helix chain 'R' and resid 2058 through 2069 Processing helix chain 'R' and resid 2071 through 2081 removed outlier: 3.657A pdb=" N LEU R2081 " --> pdb=" O ALA R2077 " (cutoff:3.500A) Processing helix chain 'R' and resid 2084 through 2097 removed outlier: 3.572A pdb=" N GLY R2097 " --> pdb=" O LYS R2093 " (cutoff:3.500A) Processing helix chain 'R' and resid 2100 through 2111 Processing helix chain 'R' and resid 2117 through 2135 removed outlier: 3.608A pdb=" N HIS R2122 " --> pdb=" O ALA R2118 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN R2123 " --> pdb=" O GLY R2119 " (cutoff:3.500A) Processing helix chain 'R' and resid 2137 through 2143 removed outlier: 4.435A pdb=" N LEU R2141 " --> pdb=" O GLU R2137 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS R2143 " --> pdb=" O GLY R2139 " (cutoff:3.500A) Processing helix chain 'R' and resid 2145 through 2157 removed outlier: 4.112A pdb=" N MET R2149 " --> pdb=" O LYS R2145 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R2154 " --> pdb=" O LEU R2150 " (cutoff:3.500A) Processing helix chain 'R' and resid 2159 through 2170 removed outlier: 4.457A pdb=" N LEU R2163 " --> pdb=" O ASN R2159 " (cutoff:3.500A) Processing helix chain 'R' and resid 2172 through 2187 removed outlier: 3.910A pdb=" N ALA R2176 " --> pdb=" O SER R2172 " (cutoff:3.500A) Processing helix chain 'R' and resid 2196 through 2208 Processing helix chain 'S' and resid 9 through 16 removed outlier: 3.655A pdb=" N THR S 13 " --> pdb=" O ASN S 10 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY S 14 " --> pdb=" O ASP S 11 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER S 15 " --> pdb=" O ASP S 12 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY S 16 " --> pdb=" O THR S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 178 Processing helix chain 'S' and resid 180 through 189 Processing helix chain 'S' and resid 398 through 406 removed outlier: 4.118A pdb=" N ARG S 402 " --> pdb=" O ASN S 398 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS S 405 " --> pdb=" O SER S 401 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS S 406 " --> pdb=" O ARG S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 420 removed outlier: 3.774A pdb=" N SER S 414 " --> pdb=" O ALA S 410 " (cutoff:3.500A) Processing helix chain 'S' and resid 423 through 440 Processing helix chain 'S' and resid 447 through 465 removed outlier: 3.621A pdb=" N TRP S 451 " --> pdb=" O GLU S 447 " (cutoff:3.500A) Processing helix chain 'S' and resid 467 through 477 Processing helix chain 'S' and resid 482 through 501 Processing helix chain 'S' and resid 509 through 530 removed outlier: 3.733A pdb=" N THR S 523 " --> pdb=" O HIS S 519 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR S 524 " --> pdb=" O ALA S 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR S 526 " --> pdb=" O LEU S 522 " (cutoff:3.500A) Processing helix chain 'S' and resid 535 through 545 Processing helix chain 'S' and resid 548 through 559 removed outlier: 3.676A pdb=" N ILE S 552 " --> pdb=" O ASP S 548 " (cutoff:3.500A) Processing helix chain 'S' and resid 560 through 571 Processing helix chain 'S' and resid 575 through 579 Processing helix chain 'S' and resid 580 through 591 Processing helix chain 'S' and resid 600 through 607 Processing helix chain 'S' and resid 607 through 616 Processing helix chain 'S' and resid 619 through 638 removed outlier: 3.702A pdb=" N ARG S 632 " --> pdb=" O GLU S 628 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU S 635 " --> pdb=" O ALA S 631 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU S 636 " --> pdb=" O ARG S 632 " (cutoff:3.500A) Processing helix chain 'S' and resid 643 through 651 Processing helix chain 'S' and resid 667 through 671 removed outlier: 3.732A pdb=" N ILE S 671 " --> pdb=" O TRP S 668 " (cutoff:3.500A) Processing helix chain 'S' and resid 679 through 701 Processing helix chain 'S' and resid 707 through 712 Processing helix chain 'S' and resid 715 through 726 Processing helix chain 'S' and resid 729 through 731 No H-bonds generated for 'chain 'S' and resid 729 through 731' Processing helix chain 'S' and resid 732 through 740 Processing helix chain 'S' and resid 740 through 747 Processing helix chain 'S' and resid 752 through 769 removed outlier: 3.528A pdb=" N SER S 769 " --> pdb=" O ASN S 765 " (cutoff:3.500A) Processing helix chain 'S' and resid 777 through 790 removed outlier: 3.692A pdb=" N ALA S 781 " --> pdb=" O THR S 777 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 785 " --> pdb=" O ALA S 781 " (cutoff:3.500A) Processing helix chain 'S' and resid 793 through 805 removed outlier: 3.546A pdb=" N PHE S 797 " --> pdb=" O THR S 793 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP S 798 " --> pdb=" O ASP S 794 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA S 799 " --> pdb=" O LEU S 795 " (cutoff:3.500A) Processing helix chain 'S' and resid 812 through 825 removed outlier: 3.661A pdb=" N GLU S 824 " --> pdb=" O LYS S 820 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET S 825 " --> pdb=" O GLN S 821 " (cutoff:3.500A) Processing helix chain 'S' and resid 829 through 849 Processing helix chain 'S' and resid 860 through 870 Processing helix chain 'S' and resid 875 through 887 removed outlier: 3.556A pdb=" N VAL S 883 " --> pdb=" O ASP S 879 " (cutoff:3.500A) Processing helix chain 'S' and resid 890 through 905 removed outlier: 4.259A pdb=" N ILE S 894 " --> pdb=" O SER S 890 " (cutoff:3.500A) Processing helix chain 'S' and resid 907 through 918 Processing helix chain 'S' and resid 919 through 940 removed outlier: 3.686A pdb=" N LYS S 925 " --> pdb=" O ALA S 921 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU S 940 " --> pdb=" O LEU S 936 " (cutoff:3.500A) Processing helix chain 'S' and resid 945 through 970 removed outlier: 3.897A pdb=" N ASP S 961 " --> pdb=" O LYS S 957 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 962 " --> pdb=" O THR S 958 " (cutoff:3.500A) Processing helix chain 'S' and resid 973 through 998 removed outlier: 3.930A pdb=" N GLU S 979 " --> pdb=" O GLN S 975 " (cutoff:3.500A) Processing helix chain 'S' and resid 1002 through 1008 removed outlier: 3.600A pdb=" N ASN S1008 " --> pdb=" O GLU S1004 " (cutoff:3.500A) Processing helix chain 'S' and resid 1008 through 1029 removed outlier: 3.838A pdb=" N VAL S1012 " --> pdb=" O ASN S1008 " (cutoff:3.500A) Processing helix chain 'S' and resid 1047 through 1060 removed outlier: 3.533A pdb=" N LYS S1051 " --> pdb=" O SER S1047 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA S1058 " --> pdb=" O ARG S1054 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU S1059 " --> pdb=" O GLN S1055 " (cutoff:3.500A) Processing helix chain 'S' and resid 1062 through 1077 Processing helix chain 'S' and resid 1080 through 1094 Processing helix chain 'S' and resid 1096 through 1116 Processing helix chain 'S' and resid 1127 through 1142 removed outlier: 3.798A pdb=" N ILE S1142 " --> pdb=" O GLN S1138 " (cutoff:3.500A) Processing helix chain 'S' and resid 1147 through 1167 removed outlier: 3.527A pdb=" N HIS S1157 " --> pdb=" O GLU S1153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET S1160 " --> pdb=" O LYS S1156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN S1167 " --> pdb=" O GLU S1163 " (cutoff:3.500A) Processing helix chain 'S' and resid 1178 through 1183 removed outlier: 4.099A pdb=" N GLY S1182 " --> pdb=" O LYS S1178 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR S1183 " --> pdb=" O ALA S1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1178 through 1183' Processing helix chain 'S' and resid 1188 through 1192 removed outlier: 4.340A pdb=" N TRP S1191 " --> pdb=" O TYR S1188 " (cutoff:3.500A) Processing helix chain 'S' and resid 1205 through 1208 removed outlier: 3.731A pdb=" N MET S1208 " --> pdb=" O GLU S1205 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1205 through 1208' Processing helix chain 'S' and resid 1209 through 1221 Processing helix chain 'S' and resid 1247 through 1265 removed outlier: 3.990A pdb=" N VAL S1251 " --> pdb=" O LEU S1247 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN S1261 " --> pdb=" O ALA S1257 " (cutoff:3.500A) Processing helix chain 'S' and resid 1267 through 1288 removed outlier: 3.852A pdb=" N ARG S1273 " --> pdb=" O GLU S1269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER S1286 " --> pdb=" O CYS S1282 " (cutoff:3.500A) Processing helix chain 'S' and resid 1292 through 1301 removed outlier: 4.380A pdb=" N LYS S1298 " --> pdb=" O THR S1294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU S1299 " --> pdb=" O LEU S1295 " (cutoff:3.500A) Processing helix chain 'S' and resid 1302 through 1336 removed outlier: 3.597A pdb=" N GLU S1325 " --> pdb=" O ILE S1321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR S1329 " --> pdb=" O GLU S1325 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE S1335 " --> pdb=" O LEU S1331 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN S1336 " --> pdb=" O HIS S1332 " (cutoff:3.500A) Processing helix chain 'S' and resid 1341 through 1350 removed outlier: 3.615A pdb=" N THR S1350 " --> pdb=" O LEU S1346 " (cutoff:3.500A) Processing helix chain 'S' and resid 1355 through 1367 removed outlier: 4.162A pdb=" N GLU S1359 " --> pdb=" O LYS S1355 " (cutoff:3.500A) Processing helix chain 'S' and resid 1371 through 1389 removed outlier: 3.519A pdb=" N ILE S1375 " --> pdb=" O ASN S1371 " (cutoff:3.500A) Processing helix chain 'S' and resid 1391 through 1414 removed outlier: 3.516A pdb=" N GLY S1395 " --> pdb=" O GLU S1391 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU S1396 " --> pdb=" O ILE S1392 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS S1397 " --> pdb=" O GLU S1393 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU S1414 " --> pdb=" O ARG S1410 " (cutoff:3.500A) Processing helix chain 'S' and resid 1418 through 1422 removed outlier: 3.836A pdb=" N VAL S1421 " --> pdb=" O PHE S1418 " (cutoff:3.500A) Processing helix chain 'S' and resid 1425 through 1429 Processing helix chain 'S' and resid 1430 through 1438 removed outlier: 4.321A pdb=" N LYS S1434 " --> pdb=" O LYS S1430 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA S1435 " --> pdb=" O ASP S1431 " (cutoff:3.500A) Processing helix chain 'S' and resid 1443 through 1454 removed outlier: 3.518A pdb=" N PHE S1454 " --> pdb=" O TYR S1450 " (cutoff:3.500A) Processing helix chain 'S' and resid 1457 through 1476 removed outlier: 3.674A pdb=" N VAL S1461 " --> pdb=" O ASP S1457 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR S1473 " --> pdb=" O LEU S1469 " (cutoff:3.500A) Processing helix chain 'S' and resid 1482 through 1502 removed outlier: 3.617A pdb=" N SER S1486 " --> pdb=" O ALA S1482 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG S1489 " --> pdb=" O ASP S1485 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG S1490 " --> pdb=" O SER S1486 " (cutoff:3.500A) Proline residue: S1492 - end of helix removed outlier: 3.877A pdb=" N GLU S1500 " --> pdb=" O ALA S1496 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET S1501 " --> pdb=" O LYS S1497 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL S1502 " --> pdb=" O ALA S1498 " (cutoff:3.500A) Processing helix chain 'S' and resid 1503 through 1505 No H-bonds generated for 'chain 'S' and resid 1503 through 1505' Processing helix chain 'S' and resid 1508 through 1521 Processing helix chain 'S' and resid 1526 through 1541 Processing helix chain 'S' and resid 1551 through 1562 removed outlier: 3.743A pdb=" N ILE S1555 " --> pdb=" O GLN S1551 " (cutoff:3.500A) Processing helix chain 'S' and resid 1569 through 1579 removed outlier: 3.760A pdb=" N HIS S1579 " --> pdb=" O TYR S1575 " (cutoff:3.500A) Processing helix chain 'S' and resid 1584 through 1589 Processing helix chain 'S' and resid 1600 through 1608 Processing helix chain 'S' and resid 1609 through 1612 removed outlier: 3.853A pdb=" N LEU S1612 " --> pdb=" O SER S1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1609 through 1612' Processing helix chain 'S' and resid 1615 through 1628 removed outlier: 4.592A pdb=" N THR S1619 " --> pdb=" O GLU S1615 " (cutoff:3.500A) Processing helix chain 'S' and resid 1630 through 1646 removed outlier: 4.012A pdb=" N LEU S1634 " --> pdb=" O SER S1630 " (cutoff:3.500A) Processing helix chain 'S' and resid 1646 through 1655 removed outlier: 3.963A pdb=" N LYS S1650 " --> pdb=" O LYS S1646 " (cutoff:3.500A) Processing helix chain 'S' and resid 1660 through 1680 removed outlier: 4.438A pdb=" N LYS S1665 " --> pdb=" O THR S1661 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU S1666 " --> pdb=" O LEU S1662 " (cutoff:3.500A) Processing helix chain 'S' and resid 1683 through 1698 removed outlier: 3.503A pdb=" N ALA S1687 " --> pdb=" O ASN S1683 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER S1693 " --> pdb=" O ALA S1689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP S1697 " --> pdb=" O SER S1693 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE S1698 " --> pdb=" O LEU S1694 " (cutoff:3.500A) Processing helix chain 'S' and resid 1701 through 1721 Processing helix chain 'S' and resid 1727 through 1755 removed outlier: 3.534A pdb=" N LYS S1731 " --> pdb=" O GLU S1727 " (cutoff:3.500A) Processing helix chain 'S' and resid 1759 through 1765 Processing helix chain 'S' and resid 1768 through 1777 Processing helix chain 'S' and resid 1779 through 1788 removed outlier: 4.025A pdb=" N ASN S1783 " --> pdb=" O HIS S1779 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE S1786 " --> pdb=" O ILE S1782 " (cutoff:3.500A) Processing helix chain 'S' and resid 1796 through 1809 removed outlier: 3.707A pdb=" N GLU S1803 " --> pdb=" O ALA S1799 " (cutoff:3.500A) Processing helix chain 'S' and resid 1811 through 1825 removed outlier: 4.213A pdb=" N VAL S1815 " --> pdb=" O ASN S1811 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS S1825 " --> pdb=" O GLU S1821 " (cutoff:3.500A) Processing helix chain 'S' and resid 1833 through 1839 removed outlier: 3.579A pdb=" N GLU S1839 " --> pdb=" O SER S1835 " (cutoff:3.500A) Processing helix chain 'S' and resid 1840 through 1842 No H-bonds generated for 'chain 'S' and resid 1840 through 1842' Processing helix chain 'S' and resid 1843 through 1856 removed outlier: 3.663A pdb=" N ARG S1847 " --> pdb=" O ASP S1843 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S1855 " --> pdb=" O TYR S1851 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG S1856 " --> pdb=" O LEU S1852 " (cutoff:3.500A) Processing helix chain 'S' and resid 1857 through 1871 removed outlier: 3.514A pdb=" N ARG S1863 " --> pdb=" O ASP S1859 " (cutoff:3.500A) Processing helix chain 'S' and resid 1882 through 1897 Processing helix chain 'S' and resid 1898 through 1907 removed outlier: 3.538A pdb=" N LEU S1905 " --> pdb=" O THR S1901 " (cutoff:3.500A) Processing helix chain 'S' and resid 1909 through 1929 Processing helix chain 'S' and resid 1934 through 1938 Processing helix chain 'S' and resid 1942 through 1954 removed outlier: 3.631A pdb=" N MET S1946 " --> pdb=" O PRO S1942 " (cutoff:3.500A) Processing helix chain 'S' and resid 1957 through 1972 removed outlier: 3.729A pdb=" N GLU S1970 " --> pdb=" O GLU S1966 " (cutoff:3.500A) Processing helix chain 'S' and resid 1975 through 1989 removed outlier: 3.553A pdb=" N LEU S1987 " --> pdb=" O LEU S1983 " (cutoff:3.500A) Processing helix chain 'S' and resid 1991 through 2002 Processing helix chain 'S' and resid 2006 through 2011 removed outlier: 3.611A pdb=" N GLN S2010 " --> pdb=" O SER S2007 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S2011 " --> pdb=" O LEU S2008 " (cutoff:3.500A) Processing helix chain 'S' and resid 2013 through 2029 removed outlier: 3.582A pdb=" N ARG S2020 " --> pdb=" O LYS S2016 " (cutoff:3.500A) Proline residue: S2025 - end of helix Processing helix chain 'S' and resid 2034 through 2051 Processing helix chain 'S' and resid 2053 through 2057 Processing helix chain 'S' and resid 2058 through 2069 Processing helix chain 'S' and resid 2071 through 2081 removed outlier: 3.658A pdb=" N LEU S2081 " --> pdb=" O ALA S2077 " (cutoff:3.500A) Processing helix chain 'S' and resid 2084 through 2097 removed outlier: 3.571A pdb=" N GLY S2097 " --> pdb=" O LYS S2093 " (cutoff:3.500A) Processing helix chain 'S' and resid 2100 through 2111 Processing helix chain 'S' and resid 2117 through 2135 removed outlier: 3.608A pdb=" N HIS S2122 " --> pdb=" O ALA S2118 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN S2123 " --> pdb=" O GLY S2119 " (cutoff:3.500A) Processing helix chain 'S' and resid 2137 through 2143 removed outlier: 4.435A pdb=" N LEU S2141 " --> pdb=" O GLU S2137 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS S2143 " --> pdb=" O GLY S2139 " (cutoff:3.500A) Processing helix chain 'S' and resid 2145 through 2157 removed outlier: 4.112A pdb=" N MET S2149 " --> pdb=" O LYS S2145 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA S2154 " --> pdb=" O LEU S2150 " (cutoff:3.500A) Processing helix chain 'S' and resid 2159 through 2170 removed outlier: 4.455A pdb=" N LEU S2163 " --> pdb=" O ASN S2159 " (cutoff:3.500A) Processing helix chain 'S' and resid 2172 through 2187 removed outlier: 3.910A pdb=" N ALA S2176 " --> pdb=" O SER S2172 " (cutoff:3.500A) Processing helix chain 'S' and resid 2196 through 2208 Processing helix chain 'W' and resid 4 through 13 removed outlier: 3.695A pdb=" N VAL W 8 " --> pdb=" O PHE W 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA W 10 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS W 11 " --> pdb=" O GLU W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 47 removed outlier: 3.850A pdb=" N SER W 43 " --> pdb=" O CYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 82 removed outlier: 3.852A pdb=" N GLN W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG W 82 " --> pdb=" O GLU W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 128 removed outlier: 3.867A pdb=" N GLN W 98 " --> pdb=" O ASP W 94 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR W 127 " --> pdb=" O ASN W 123 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU W 128 " --> pdb=" O CYS W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 151 removed outlier: 3.557A pdb=" N ARG W 151 " --> pdb=" O LEU W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 184 removed outlier: 3.701A pdb=" N GLN W 182 " --> pdb=" O GLY W 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS W 183 " --> pdb=" O GLU W 179 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU W 184 " --> pdb=" O GLU W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 203 removed outlier: 3.651A pdb=" N TYR W 201 " --> pdb=" O SER W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 234 Processing helix chain 'W' and resid 236 through 252 removed outlier: 3.535A pdb=" N MET W 247 " --> pdb=" O SER W 243 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 259 removed outlier: 3.612A pdb=" N LEU W 256 " --> pdb=" O ILE W 252 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA W 257 " --> pdb=" O LEU W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 288 through 307 removed outlier: 3.670A pdb=" N VAL W 302 " --> pdb=" O LEU W 298 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 333 removed outlier: 3.614A pdb=" N MET W 329 " --> pdb=" O PRO W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 346 removed outlier: 3.721A pdb=" N GLU W 340 " --> pdb=" O GLU W 336 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS W 341 " --> pdb=" O ASP W 337 " (cutoff:3.500A) Processing helix chain 'W' and resid 354 through 360 removed outlier: 4.508A pdb=" N GLN W 359 " --> pdb=" O SER W 356 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN W 360 " --> pdb=" O LYS W 357 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 378 removed outlier: 3.885A pdb=" N LEU W 375 " --> pdb=" O PHE W 371 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 393 removed outlier: 3.802A pdb=" N ALA W 392 " --> pdb=" O LEU W 388 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 404 removed outlier: 3.766A pdb=" N LYS W 402 " --> pdb=" O HIS W 398 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 414 removed outlier: 3.626A pdb=" N ALA W 410 " --> pdb=" O ASP W 406 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA W 411 " --> pdb=" O VAL W 407 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU W 414 " --> pdb=" O ALA W 410 " (cutoff:3.500A) Processing helix chain 'W' and resid 440 through 447 removed outlier: 3.570A pdb=" N ASN W 443 " --> pdb=" O ASP W 440 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU W 445 " --> pdb=" O ASP W 442 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU W 446 " --> pdb=" O ASN W 443 " (cutoff:3.500A) Processing helix chain 'W' and resid 468 through 472 removed outlier: 3.745A pdb=" N SER W 471 " --> pdb=" O ASP W 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE W 472 " --> pdb=" O GLN W 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 468 through 472' Processing helix chain 'W' and resid 481 through 498 removed outlier: 3.565A pdb=" N THR W 498 " --> pdb=" O LEU W 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 501 through 527 removed outlier: 3.724A pdb=" N ASP W 521 " --> pdb=" O HIS W 517 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL W 523 " --> pdb=" O PHE W 519 " (cutoff:3.500A) Proline residue: W 524 - end of helix Processing helix chain 'W' and resid 534 through 556 removed outlier: 3.743A pdb=" N ALA W 538 " --> pdb=" O LEU W 534 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA W 539 " --> pdb=" O PRO W 535 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU W 553 " --> pdb=" O ALA W 549 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR W 554 " --> pdb=" O HIS W 550 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY W 556 " --> pdb=" O LEU W 552 " (cutoff:3.500A) Processing helix chain 'W' and resid 557 through 560 Processing helix chain 'W' and resid 574 through 576 No H-bonds generated for 'chain 'W' and resid 574 through 576' Processing helix chain 'W' and resid 577 through 604 removed outlier: 3.504A pdb=" N ARG W 582 " --> pdb=" O VAL W 578 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS W 588 " --> pdb=" O LEU W 584 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE W 589 " --> pdb=" O GLY W 585 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN W 592 " --> pdb=" O CYS W 588 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU W 599 " --> pdb=" O ALA W 595 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU W 602 " --> pdb=" O GLY W 598 " (cutoff:3.500A) Processing helix chain 'W' and resid 605 through 611 removed outlier: 3.994A pdb=" N ARG W 608 " --> pdb=" O SER W 605 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN W 609 " --> pdb=" O SER W 606 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER W 611 " --> pdb=" O ARG W 608 " (cutoff:3.500A) Processing helix chain 'W' and resid 615 through 641 removed outlier: 3.502A pdb=" N ALA W 625 " --> pdb=" O ALA W 621 " (cutoff:3.500A) Processing helix chain 'W' and resid 645 through 670 removed outlier: 3.610A pdb=" N GLU W 663 " --> pdb=" O THR W 659 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL W 664 " --> pdb=" O ALA W 660 " (cutoff:3.500A) Processing helix chain 'W' and resid 675 through 693 removed outlier: 3.867A pdb=" N TYR W 683 " --> pdb=" O GLY W 679 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR W 688 " --> pdb=" O SER W 684 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL W 689 " --> pdb=" O LEU W 685 " (cutoff:3.500A) Processing helix chain 'W' and resid 702 through 711 removed outlier: 3.630A pdb=" N ASN W 706 " --> pdb=" O GLU W 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS W 707 " --> pdb=" O GLU W 703 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS W 708 " --> pdb=" O SER W 704 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR W 709 " --> pdb=" O LYS W 705 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU W 711 " --> pdb=" O LYS W 707 " (cutoff:3.500A) Processing helix chain 'W' and resid 712 through 717 removed outlier: 3.670A pdb=" N TYR W 716 " --> pdb=" O GLU W 712 " (cutoff:3.500A) Processing helix chain 'W' and resid 719 through 730 removed outlier: 3.610A pdb=" N PHE W 723 " --> pdb=" O LYS W 719 " (cutoff:3.500A) Processing helix chain 'W' and resid 733 through 742 removed outlier: 3.678A pdb=" N ALA W 742 " --> pdb=" O GLY W 738 " (cutoff:3.500A) Processing helix chain 'W' and resid 746 through 752 Processing helix chain 'W' and resid 753 through 765 Processing helix chain 'W' and resid 768 through 778 Processing helix chain 'X' and resid 4 through 13 removed outlier: 3.696A pdb=" N VAL X 8 " --> pdb=" O PHE X 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA X 10 " --> pdb=" O THR X 6 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS X 11 " --> pdb=" O GLU X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 47 removed outlier: 3.849A pdb=" N SER X 43 " --> pdb=" O CYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 82 removed outlier: 3.853A pdb=" N GLN X 57 " --> pdb=" O MET X 53 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG X 82 " --> pdb=" O GLU X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 128 removed outlier: 3.867A pdb=" N GLN X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR X 127 " --> pdb=" O ASN X 123 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 151 removed outlier: 3.556A pdb=" N ARG X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 184 removed outlier: 3.701A pdb=" N GLN X 182 " --> pdb=" O GLY X 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS X 183 " --> pdb=" O GLU X 179 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU X 184 " --> pdb=" O GLU X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 203 removed outlier: 3.652A pdb=" N TYR X 201 " --> pdb=" O SER X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 223 through 234 Processing helix chain 'X' and resid 236 through 252 removed outlier: 3.535A pdb=" N MET X 247 " --> pdb=" O SER X 243 " (cutoff:3.500A) Processing helix chain 'X' and resid 252 through 259 removed outlier: 3.612A pdb=" N LEU X 256 " --> pdb=" O ILE X 252 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 307 removed outlier: 3.671A pdb=" N VAL X 302 " --> pdb=" O LEU X 298 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 333 removed outlier: 3.614A pdb=" N MET X 329 " --> pdb=" O PRO X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 334 through 346 removed outlier: 3.720A pdb=" N GLU X 340 " --> pdb=" O GLU X 336 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS X 341 " --> pdb=" O ASP X 337 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 360 removed outlier: 4.509A pdb=" N GLN X 359 " --> pdb=" O SER X 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN X 360 " --> pdb=" O LYS X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 361 through 378 removed outlier: 3.885A pdb=" N LEU X 375 " --> pdb=" O PHE X 371 " (cutoff:3.500A) Processing helix chain 'X' and resid 386 through 393 removed outlier: 3.802A pdb=" N ALA X 392 " --> pdb=" O LEU X 388 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 404 removed outlier: 3.767A pdb=" N LYS X 402 " --> pdb=" O HIS X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 414 removed outlier: 3.626A pdb=" N ALA X 410 " --> pdb=" O ASP X 406 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA X 411 " --> pdb=" O VAL X 407 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU X 414 " --> pdb=" O ALA X 410 " (cutoff:3.500A) Processing helix chain 'X' and resid 440 through 447 removed outlier: 3.570A pdb=" N ASN X 443 " --> pdb=" O ASP X 440 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU X 445 " --> pdb=" O ASP X 442 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU X 446 " --> pdb=" O ASN X 443 " (cutoff:3.500A) Processing helix chain 'X' and resid 468 through 472 removed outlier: 3.744A pdb=" N SER X 471 " --> pdb=" O ASP X 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE X 472 " --> pdb=" O GLN X 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 468 through 472' Processing helix chain 'X' and resid 481 through 498 removed outlier: 3.565A pdb=" N THR X 498 " --> pdb=" O LEU X 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 501 through 527 removed outlier: 3.724A pdb=" N ASP X 521 " --> pdb=" O HIS X 517 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL X 523 " --> pdb=" O PHE X 519 " (cutoff:3.500A) Proline residue: X 524 - end of helix Processing helix chain 'X' and resid 534 through 556 removed outlier: 3.743A pdb=" N ALA X 538 " --> pdb=" O LEU X 534 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA X 539 " --> pdb=" O PRO X 535 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU X 553 " --> pdb=" O ALA X 549 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR X 554 " --> pdb=" O HIS X 550 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY X 556 " --> pdb=" O LEU X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 557 through 560 Processing helix chain 'X' and resid 574 through 576 No H-bonds generated for 'chain 'X' and resid 574 through 576' Processing helix chain 'X' and resid 577 through 604 removed outlier: 3.504A pdb=" N ARG X 582 " --> pdb=" O VAL X 578 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS X 588 " --> pdb=" O LEU X 584 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE X 589 " --> pdb=" O GLY X 585 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN X 592 " --> pdb=" O CYS X 588 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU X 599 " --> pdb=" O ALA X 595 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU X 602 " --> pdb=" O GLY X 598 " (cutoff:3.500A) Processing helix chain 'X' and resid 605 through 611 removed outlier: 3.995A pdb=" N ARG X 608 " --> pdb=" O SER X 605 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN X 609 " --> pdb=" O SER X 606 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER X 611 " --> pdb=" O ARG X 608 " (cutoff:3.500A) Processing helix chain 'X' and resid 615 through 641 removed outlier: 3.500A pdb=" N ALA X 625 " --> pdb=" O ALA X 621 " (cutoff:3.500A) Processing helix chain 'X' and resid 645 through 670 removed outlier: 3.610A pdb=" N GLU X 663 " --> pdb=" O THR X 659 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL X 664 " --> pdb=" O ALA X 660 " (cutoff:3.500A) Processing helix chain 'X' and resid 675 through 693 removed outlier: 3.867A pdb=" N TYR X 683 " --> pdb=" O GLY X 679 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR X 688 " --> pdb=" O SER X 684 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL X 689 " --> pdb=" O LEU X 685 " (cutoff:3.500A) Processing helix chain 'X' and resid 702 through 711 removed outlier: 3.628A pdb=" N ASN X 706 " --> pdb=" O GLU X 702 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS X 707 " --> pdb=" O GLU X 703 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS X 708 " --> pdb=" O SER X 704 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR X 709 " --> pdb=" O LYS X 705 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU X 711 " --> pdb=" O LYS X 707 " (cutoff:3.500A) Processing helix chain 'X' and resid 712 through 717 removed outlier: 3.671A pdb=" N TYR X 716 " --> pdb=" O GLU X 712 " (cutoff:3.500A) Processing helix chain 'X' and resid 719 through 730 removed outlier: 3.611A pdb=" N PHE X 723 " --> pdb=" O LYS X 719 " (cutoff:3.500A) Processing helix chain 'X' and resid 733 through 742 removed outlier: 3.678A pdb=" N ALA X 742 " --> pdb=" O GLY X 738 " (cutoff:3.500A) Processing helix chain 'X' and resid 746 through 752 Processing helix chain 'X' and resid 753 through 765 Processing helix chain 'X' and resid 768 through 778 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.431A pdb=" N PHE B 62 " --> pdb=" O TRP B 137 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG B 139 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 64 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 170 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 530 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 225 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 247 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.431A pdb=" N PHE B 62 " --> pdb=" O TRP B 137 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG B 139 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 64 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 158 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 43 removed outlier: 6.431A pdb=" N PHE C 62 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ARG C 139 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C 64 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 170 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 530 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 225 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 247 " --> pdb=" O VAL C 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 43 removed outlier: 6.431A pdb=" N PHE C 62 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ARG C 139 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C 64 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 158 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE C 162 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 4 through 7 removed outlier: 5.317A pdb=" N VAL R 33 " --> pdb=" O THR R 392 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR R 392 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU R 35 " --> pdb=" O CYS R 390 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N CYS R 390 " --> pdb=" O LEU R 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL R 37 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER R 384 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 365 " --> pdb=" O LEU R 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 51 through 55 Processing sheet with id=AA7, first strand: chain 'R' and resid 87 through 93 removed outlier: 7.073A pdb=" N GLY R 102 " --> pdb=" O ASP R 88 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL R 90 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU R 100 " --> pdb=" O VAL R 90 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU R 92 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE R 98 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN R 107 " --> pdb=" O GLU R 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS R 112 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR R 118 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 136 through 143 removed outlier: 6.540A pdb=" N LEU R 156 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU R 139 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU R 154 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE R 141 " --> pdb=" O TYR R 152 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR R 152 " --> pdb=" O ILE R 141 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR R 151 " --> pdb=" O ASN R 166 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN R 166 " --> pdb=" O TYR R 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 206 through 211 removed outlier: 4.222A pdb=" N ALA R 229 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS R 228 " --> pdb=" O ASP R 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP R 249 " --> pdb=" O CYS R 228 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE R 230 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU R 247 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS R 232 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 256 through 261 removed outlier: 7.203A pdb=" N LEU R 269 " --> pdb=" O LYS R 257 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE R 259 " --> pdb=" O PHE R 267 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE R 267 " --> pdb=" O PHE R 259 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL R 274 " --> pdb=" O ASP R 270 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU R 275 " --> pdb=" O TRP R 289 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL R 294 " --> pdb=" O ALA R 324 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA R 324 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU R 296 " --> pdb=" O LEU R 322 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR R 300 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS R 318 " --> pdb=" O THR R 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS R 331 " --> pdb=" O GLU R 348 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU R 348 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU R 333 " --> pdb=" O SER R 346 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER R 346 " --> pdb=" O LEU R 333 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL R 335 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU R 342 " --> pdb=" O SER R 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 removed outlier: 5.318A pdb=" N VAL S 33 " --> pdb=" O THR S 392 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR S 392 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU S 35 " --> pdb=" O CYS S 390 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N CYS S 390 " --> pdb=" O LEU S 35 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL S 37 " --> pdb=" O LEU S 388 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER S 384 " --> pdb=" O SER S 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE S 365 " --> pdb=" O LEU S 391 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 51 through 55 Processing sheet with id=AB4, first strand: chain 'S' and resid 87 through 93 removed outlier: 7.072A pdb=" N GLY S 102 " --> pdb=" O ASP S 88 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL S 90 " --> pdb=" O LEU S 100 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU S 100 " --> pdb=" O VAL S 90 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU S 92 " --> pdb=" O PHE S 98 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE S 98 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN S 107 " --> pdb=" O GLU S 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS S 112 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR S 118 " --> pdb=" O HIS S 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 136 through 143 removed outlier: 6.540A pdb=" N LEU S 156 " --> pdb=" O GLN S 137 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU S 139 " --> pdb=" O LEU S 154 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU S 154 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE S 141 " --> pdb=" O TYR S 152 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR S 152 " --> pdb=" O ILE S 141 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR S 151 " --> pdb=" O ASN S 166 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN S 166 " --> pdb=" O TYR S 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 206 through 211 removed outlier: 4.222A pdb=" N ALA S 229 " --> pdb=" O GLY S 224 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS S 228 " --> pdb=" O ASP S 249 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP S 249 " --> pdb=" O CYS S 228 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE S 230 " --> pdb=" O LEU S 247 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU S 247 " --> pdb=" O PHE S 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS S 232 " --> pdb=" O LYS S 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 256 through 261 removed outlier: 7.204A pdb=" N LEU S 269 " --> pdb=" O LYS S 257 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE S 259 " --> pdb=" O PHE S 267 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE S 267 " --> pdb=" O PHE S 259 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL S 274 " --> pdb=" O ASP S 270 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU S 275 " --> pdb=" O TRP S 289 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL S 294 " --> pdb=" O ALA S 324 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA S 324 " --> pdb=" O VAL S 294 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU S 296 " --> pdb=" O LEU S 322 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR S 300 " --> pdb=" O LYS S 318 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS S 318 " --> pdb=" O THR S 300 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS S 331 " --> pdb=" O GLU S 348 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU S 348 " --> pdb=" O LYS S 331 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU S 333 " --> pdb=" O SER S 346 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER S 346 " --> pdb=" O LEU S 333 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL S 335 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU S 342 " --> pdb=" O SER S 337 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 185 through 188 Processing sheet with id=AB9, first strand: chain 'W' and resid 422 through 425 removed outlier: 3.774A pdb=" N CYS W 477 " --> pdb=" O ILE W 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 185 through 188 Processing sheet with id=AC2, first strand: chain 'X' and resid 422 through 425 removed outlier: 3.773A pdb=" N CYS X 477 " --> pdb=" O ILE X 425 " (cutoff:3.500A) 3244 hydrogen bonds defined for protein. 9474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.49 Time building geometry restraints manager: 17.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18479 1.34 - 1.46: 11644 1.46 - 1.58: 27681 1.58 - 1.70: 0 1.70 - 1.82: 456 Bond restraints: 58260 Sorted by residual: bond pdb=" SD MET S 983 " pdb=" CE MET S 983 " ideal model delta sigma weight residual 1.791 1.763 0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CA PHE B 312 " pdb=" CB PHE B 312 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.61e-02 3.86e+03 1.23e+00 bond pdb=" SD MET R 983 " pdb=" CE MET R 983 " ideal model delta sigma weight residual 1.791 1.763 0.028 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CA PHE C 312 " pdb=" CB PHE C 312 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.61e-02 3.86e+03 1.21e+00 bond pdb=" CA ILE C 240 " pdb=" CB ILE C 240 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.03e+00 ... (remaining 58255 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.22: 987 105.22 - 112.43: 30429 112.43 - 119.64: 19966 119.64 - 126.86: 26772 126.86 - 134.07: 718 Bond angle restraints: 78872 Sorted by residual: angle pdb=" C THR B 414 " pdb=" N ILE B 415 " pdb=" CA ILE B 415 " ideal model delta sigma weight residual 120.33 123.50 -3.17 8.00e-01 1.56e+00 1.57e+01 angle pdb=" C THR C 414 " pdb=" N ILE C 415 " pdb=" CA ILE C 415 " ideal model delta sigma weight residual 120.33 123.42 -3.09 8.00e-01 1.56e+00 1.49e+01 angle pdb=" N ILE R 252 " pdb=" CA ILE R 252 " pdb=" C ILE R 252 " ideal model delta sigma weight residual 111.45 108.30 3.15 9.30e-01 1.16e+00 1.15e+01 angle pdb=" N ILE S 252 " pdb=" CA ILE S 252 " pdb=" C ILE S 252 " ideal model delta sigma weight residual 111.45 108.33 3.12 9.30e-01 1.16e+00 1.13e+01 angle pdb=" C PHE S1418 " pdb=" N GLN S1419 " pdb=" CA GLN S1419 " ideal model delta sigma weight residual 120.26 124.54 -4.28 1.34e+00 5.57e-01 1.02e+01 ... (remaining 78867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 33921 16.08 - 32.16: 1425 32.16 - 48.24: 304 48.24 - 64.31: 36 64.31 - 80.39: 34 Dihedral angle restraints: 35720 sinusoidal: 14560 harmonic: 21160 Sorted by residual: dihedral pdb=" CA PRO R1942 " pdb=" C PRO R1942 " pdb=" N LYS R1943 " pdb=" CA LYS R1943 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PRO S1942 " pdb=" C PRO S1942 " pdb=" N LYS S1943 " pdb=" CA LYS S1943 " ideal model delta harmonic sigma weight residual -180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA HIS S1579 " pdb=" C HIS S1579 " pdb=" N VAL S1580 " pdb=" CA VAL S1580 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 35717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 5994 0.033 - 0.065: 2434 0.065 - 0.098: 503 0.098 - 0.131: 230 0.131 - 0.163: 9 Chirality restraints: 9170 Sorted by residual: chirality pdb=" CA ILE S1581 " pdb=" N ILE S1581 " pdb=" C ILE S1581 " pdb=" CB ILE S1581 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE R1581 " pdb=" N ILE R1581 " pdb=" C ILE R1581 " pdb=" CB ILE R1581 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL X 433 " pdb=" N VAL X 433 " pdb=" C VAL X 433 " pdb=" CB VAL X 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 9167 not shown) Planarity restraints: 9956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 338 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO R 339 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 339 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 339 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU S 338 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO S 339 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO S 339 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 339 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 287 " 0.010 2.00e-02 2.50e+03 1.20e-02 3.60e+00 pdb=" CG TRP R 287 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP R 287 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP R 287 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 287 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 287 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 287 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP R 287 " -0.004 2.00e-02 2.50e+03 ... (remaining 9953 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 380 2.65 - 3.22: 52188 3.22 - 3.78: 85835 3.78 - 4.34: 117548 4.34 - 4.90: 191228 Nonbonded interactions: 447179 Sorted by model distance: nonbonded pdb=" OG SER W 288 " pdb=" OE1 GLU W 291 " model vdw 2.093 2.440 nonbonded pdb=" OG SER X 288 " pdb=" OE1 GLU X 291 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR S1527 " pdb=" O LEU S1591 " model vdw 2.146 2.440 nonbonded pdb=" OH TYR R1527 " pdb=" O LEU R1591 " model vdw 2.147 2.440 nonbonded pdb=" O PRO R2083 " pdb=" ND2 ASN S 491 " model vdw 2.171 2.520 ... (remaining 447174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'W' 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.320 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 110.130 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 0.028 58260 Z= 0.127 Angle : 0.539 7.888 78872 Z= 0.335 Chirality : 0.038 0.163 9170 Planarity : 0.003 0.048 9956 Dihedral : 10.055 80.393 21908 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7144 helix: 1.06 (0.08), residues: 4104 sheet: -0.34 (0.22), residues: 546 loop : -0.98 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP S1369 HIS 0.009 0.001 HIS S 699 PHE 0.024 0.001 PHE S 987 TYR 0.015 0.001 TYR R 336 ARG 0.005 0.000 ARG W 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 865 time to evaluate : 4.971 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 outliers start: 0 outliers final: 0 residues processed: 865 average time/residue: 0.5891 time to fit residues: 859.0957 Evaluate side-chains 463 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 4.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 601 optimal weight: 20.0000 chunk 539 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 364 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 558 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 415 optimal weight: 0.9990 chunk 646 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 508 HIS ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN C 304 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 GLN R 327 ASN R 589 ASN R 691 ASN ** R1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1574 GLN ** R2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R2186 HIS S 327 ASN ** S 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 691 ASN ** S1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1574 GLN S1742 GLN ** S2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 452 ASN W 517 HIS ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 452 ASN X 517 HIS X 557 HIS X 632 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 58260 Z= 0.205 Angle : 0.619 11.253 78872 Z= 0.310 Chirality : 0.041 0.217 9170 Planarity : 0.004 0.076 9956 Dihedral : 4.273 57.623 7596 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 5.97 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7144 helix: 1.25 (0.08), residues: 4228 sheet: -0.02 (0.22), residues: 548 loop : -1.02 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 289 HIS 0.011 0.001 HIS W 557 PHE 0.030 0.002 PHE R 721 TYR 0.026 0.002 TYR S 805 ARG 0.010 0.001 ARG S1539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 490 time to evaluate : 5.025 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 outliers start: 76 outliers final: 39 residues processed: 535 average time/residue: 0.5347 time to fit residues: 495.8705 Evaluate side-chains 418 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 379 time to evaluate : 4.956 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4168 time to fit residues: 37.7401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 359 optimal weight: 0.2980 chunk 200 optimal weight: 5.9990 chunk 538 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 647 optimal weight: 0.0770 chunk 699 optimal weight: 0.7980 chunk 576 optimal weight: 5.9990 chunk 642 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 519 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 508 HIS ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 GLN R 473 ASN ** R 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 765 ASN R1169 GLN R1424 GLN ** R2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 473 ASN ** S 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 555 GLN S 589 ASN S 648 GLN S 765 ASN ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1664 ASN S1721 ASN S1808 ASN ** S2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 ASN W 113 GLN ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN X 113 GLN X 557 HIS ** X 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58260 Z= 0.189 Angle : 0.573 13.934 78872 Z= 0.285 Chirality : 0.040 0.241 9170 Planarity : 0.004 0.103 9956 Dihedral : 4.227 54.002 7596 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.83 % Allowed : 7.73 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7144 helix: 1.34 (0.08), residues: 4240 sheet: 0.06 (0.21), residues: 582 loop : -0.95 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 451 HIS 0.007 0.001 HIS X 398 PHE 0.033 0.002 PHE W 115 TYR 0.046 0.001 TYR R1635 ARG 0.010 0.000 ARG W 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 423 time to evaluate : 5.067 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 outliers start: 54 outliers final: 15 residues processed: 465 average time/residue: 0.5344 time to fit residues: 435.7593 Evaluate side-chains 377 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 362 time to evaluate : 5.028 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4234 time to fit residues: 18.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 639 optimal weight: 7.9990 chunk 486 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 434 optimal weight: 0.9980 chunk 650 optimal weight: 5.9990 chunk 688 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 chunk 616 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 458 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN C 493 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS R 433 HIS ** R 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 648 GLN ** R1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1285 HIS R1602 GLN R1664 ASN R2094 ASN R2169 ASN S 147 ASN S 327 ASN S 433 HIS ** S 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 690 ASN S 751 GLN S1169 GLN S1424 GLN ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2010 GLN ** S2019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2094 ASN S2169 ASN W 123 ASN W 452 ASN W 470 HIS ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 541 HIS ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN X 452 ASN X 470 HIS X 541 HIS ** X 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 58260 Z= 0.410 Angle : 0.779 14.723 78872 Z= 0.393 Chirality : 0.046 0.331 9170 Planarity : 0.005 0.128 9956 Dihedral : 4.785 46.585 7596 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.71 % Allowed : 9.17 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.10), residues: 7144 helix: 0.75 (0.08), residues: 4244 sheet: 0.01 (0.21), residues: 588 loop : -0.99 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 137 HIS 0.013 0.002 HIS X 631 PHE 0.054 0.003 PHE W 697 TYR 0.037 0.003 TYR R1006 ARG 0.024 0.001 ARG W 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 402 time to evaluate : 5.005 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 outliers start: 111 outliers final: 50 residues processed: 483 average time/residue: 0.5334 time to fit residues: 452.8209 Evaluate side-chains 379 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 329 time to evaluate : 5.025 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 50 outliers final: 1 residues processed: 50 average time/residue: 0.4171 time to fit residues: 46.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 573 optimal weight: 8.9990 chunk 390 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 512 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 587 optimal weight: 0.9990 chunk 475 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 617 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 529 GLN B 539 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN C 458 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 ASN ** R 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1602 GLN S2010 GLN ** S2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2186 HIS ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 641 GLN ** X 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 641 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 58260 Z= 0.179 Angle : 0.598 13.145 78872 Z= 0.296 Chirality : 0.041 0.359 9170 Planarity : 0.003 0.052 9956 Dihedral : 4.466 44.830 7596 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.76 % Allowed : 10.19 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 7144 helix: 1.23 (0.08), residues: 4218 sheet: 0.23 (0.22), residues: 568 loop : -0.92 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP S 287 HIS 0.006 0.001 HIS R 699 PHE 0.037 0.002 PHE W 115 TYR 0.028 0.001 TYR S1238 ARG 0.004 0.000 ARG S1717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 355 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 12 residues processed: 394 average time/residue: 0.5339 time to fit residues: 373.7531 Evaluate side-chains 343 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 331 time to evaluate : 4.974 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4623 time to fit residues: 17.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 231 optimal weight: 1.9990 chunk 619 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 404 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 688 optimal weight: 0.3980 chunk 571 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 361 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 391 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 327 ASN R 357 GLN R 433 HIS R 461 ASN R 677 GLN ** R1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1023 HIS R1167 GLN S 574 ASN S 677 GLN ** S1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1023 HIS ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 58260 Z= 0.150 Angle : 0.581 14.680 78872 Z= 0.282 Chirality : 0.040 0.357 9170 Planarity : 0.003 0.054 9956 Dihedral : 4.299 42.221 7596 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.71 % Allowed : 10.73 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 7144 helix: 1.45 (0.08), residues: 4230 sheet: 0.33 (0.22), residues: 568 loop : -0.88 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 233 HIS 0.012 0.001 HIS S 405 PHE 0.023 0.001 PHE W 49 TYR 0.029 0.001 TYR S1635 ARG 0.003 0.000 ARG W 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 366 time to evaluate : 5.011 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 outliers start: 46 outliers final: 20 residues processed: 402 average time/residue: 0.5263 time to fit residues: 371.8287 Evaluate side-chains 353 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 333 time to evaluate : 5.026 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4186 time to fit residues: 22.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 664 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 392 optimal weight: 2.9990 chunk 503 optimal weight: 10.0000 chunk 389 optimal weight: 1.9990 chunk 579 optimal weight: 5.9990 chunk 384 optimal weight: 0.9990 chunk 686 optimal weight: 0.5980 chunk 429 optimal weight: 0.0470 chunk 418 optimal weight: 0.0040 chunk 316 optimal weight: 0.7980 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 461 ASN ** R 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 433 HIS S 461 ASN ** S1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 HIS ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 632 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 58260 Z= 0.141 Angle : 0.579 17.247 78872 Z= 0.279 Chirality : 0.040 0.383 9170 Planarity : 0.003 0.055 9956 Dihedral : 4.180 39.537 7596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.54 % Allowed : 11.34 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.02 (0.10), residues: 7144 helix: 1.57 (0.08), residues: 4216 sheet: 0.37 (0.22), residues: 580 loop : -0.85 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 480 HIS 0.010 0.001 HIS S1019 PHE 0.033 0.001 PHE W 115 TYR 0.026 0.001 TYR S1635 ARG 0.009 0.000 ARG R1539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 351 time to evaluate : 4.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 374 average time/residue: 0.5374 time to fit residues: 353.8778 Evaluate side-chains 336 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 323 time to evaluate : 4.984 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4547 time to fit residues: 17.8684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 424 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 409 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 436 optimal weight: 0.9980 chunk 467 optimal weight: 0.4980 chunk 339 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 539 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 493 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 461 ASN R 574 ASN R 629 GLN ** R1326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58260 Z= 0.182 Angle : 0.591 15.095 78872 Z= 0.286 Chirality : 0.040 0.396 9170 Planarity : 0.003 0.056 9956 Dihedral : 4.174 36.008 7596 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.52 % Allowed : 11.57 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 7144 helix: 1.57 (0.08), residues: 4224 sheet: 0.29 (0.22), residues: 578 loop : -0.83 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 353 HIS 0.023 0.001 HIS X 176 PHE 0.038 0.002 PHE C 302 TYR 0.021 0.001 TYR S1635 ARG 0.006 0.000 ARG R1539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 338 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 365 average time/residue: 0.5535 time to fit residues: 354.6167 Evaluate side-chains 345 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 327 time to evaluate : 4.994 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4360 time to fit residues: 21.7804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 624 optimal weight: 1.9990 chunk 657 optimal weight: 0.5980 chunk 599 optimal weight: 0.9990 chunk 639 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 502 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 577 optimal weight: 3.9990 chunk 604 optimal weight: 20.0000 chunk 637 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN ** R1326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1603 ASN ** R2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 690 ASN ** S1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1284 GLN ** S1326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 58260 Z= 0.203 Angle : 0.617 14.331 78872 Z= 0.299 Chirality : 0.041 0.387 9170 Planarity : 0.003 0.057 9956 Dihedral : 4.225 31.859 7596 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.28 % Allowed : 12.05 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.98 (0.10), residues: 7144 helix: 1.54 (0.08), residues: 4206 sheet: 0.28 (0.22), residues: 574 loop : -0.84 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 137 HIS 0.022 0.001 HIS W 176 PHE 0.030 0.002 PHE C 348 TYR 0.025 0.001 TYR R1562 ARG 0.011 0.000 ARG R1563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 347 time to evaluate : 4.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 356 average time/residue: 0.5426 time to fit residues: 339.0760 Evaluate side-chains 331 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 323 time to evaluate : 4.987 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4213 time to fit residues: 13.3977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 419 optimal weight: 1.9990 chunk 676 optimal weight: 1.9990 chunk 412 optimal weight: 0.8980 chunk 320 optimal weight: 4.9990 chunk 470 optimal weight: 1.9990 chunk 709 optimal weight: 0.5980 chunk 652 optimal weight: 0.9980 chunk 564 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 436 optimal weight: 0.9980 chunk 346 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1133 HIS R1284 GLN ** R1326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1603 ASN ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 507 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 58260 Z= 0.165 Angle : 0.621 19.567 78872 Z= 0.295 Chirality : 0.041 0.389 9170 Planarity : 0.003 0.057 9956 Dihedral : 4.190 29.891 7596 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.19 % Allowed : 12.31 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7144 helix: 1.61 (0.08), residues: 4210 sheet: 0.32 (0.22), residues: 574 loop : -0.83 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 137 HIS 0.010 0.001 HIS S1053 PHE 0.028 0.001 PHE C 302 TYR 0.022 0.001 TYR S1635 ARG 0.010 0.000 ARG S1764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14288 Ramachandran restraints generated. 7144 Oldfield, 0 Emsley, 7144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 340 time to evaluate : 5.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 348 average time/residue: 0.5352 time to fit residues: 331.5613 Evaluate side-chains 332 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 326 time to evaluate : 4.984 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4308 time to fit residues: 11.8093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 712 random chunks: chunk 448 optimal weight: 1.9990 chunk 601 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 520 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 565 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 580 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 473 ASN ** R1326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R2010 GLN ** R2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 473 ASN ** S1491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.086153 restraints weight = 303287.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083362 restraints weight = 205214.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.083589 restraints weight = 180283.175| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 58260 Z= 0.150 Angle : 0.620 19.796 78872 Z= 0.292 Chirality : 0.040 0.383 9170 Planarity : 0.003 0.059 9956 Dihedral : 4.125 29.579 7596 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.06 % Allowed : 12.72 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.10), residues: 7144 helix: 1.66 (0.08), residues: 4212 sheet: 0.37 (0.22), residues: 574 loop : -0.81 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 137 HIS 0.009 0.001 HIS S1053 PHE 0.028 0.001 PHE C 348 TYR 0.024 0.001 TYR X 201 ARG 0.008 0.000 ARG R1847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9148.69 seconds wall clock time: 165 minutes 4.17 seconds (9904.17 seconds total)