Starting phenix.real_space_refine (version: dev) on Mon Apr 4 15:04:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozo_13130/04_2022/7ozo_13130.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.935 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 455": "OD1" <-> "OD2" Residue "N PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 221": "OD1" <-> "OD2" Residue "O TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 112": "OD1" <-> "OD2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 54330 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 42, 'TRANS': 989, 'PCIS': 1} Chain breaks: 6 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 9, 'TRANS': 160, 'PCIS': 1} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 42, 'TRANS': 989, 'PCIS': 1} Chain breaks: 6 Chain: "N" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "O" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "Q" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "R" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "S" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 9, 'TRANS': 160, 'PCIS': 1} Chain: "T" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "U" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "V" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "W" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "X" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17106 SG CYS C 88 110.833 62.048 14.810 1.00 88.38 S ATOM 17119 SG CYS C 90 107.907 64.011 13.282 1.00 96.15 S ATOM 17154 SG CYS C 94 108.066 60.694 12.146 1.00 91.04 S ATOM 17176 SG CYS C 97 107.328 60.749 15.562 1.00 91.66 S ATOM 24473 SG CYS I 17 24.539 43.044 99.997 1.00113.62 S ATOM 24497 SG CYS I 20 23.294 46.096 98.277 1.00113.40 S ATOM 24658 SG CYS I 39 25.806 46.385 101.253 1.00119.61 S ATOM 24683 SG CYS I 42 22.186 45.472 101.832 1.00115.46 S ATOM 25035 SG CYS I 86 50.252 11.048 87.504 1.00 96.86 S ATOM 25059 SG CYS I 89 47.588 9.306 85.327 1.00 99.62 S ATOM 25263 SG CYS I 114 49.977 12.014 83.864 1.00 90.30 S ATOM 25298 SG CYS I 119 47.163 12.872 86.198 1.00 98.27 S ATOM 25408 SG CYS J 7 95.886 38.182 35.465 1.00 53.15 S ATOM 25432 SG CYS J 10 99.443 37.196 34.354 1.00 45.28 S ATOM 25696 SG CYS J 44 97.689 35.363 37.208 1.00 44.27 S ATOM 25702 SG CYS J 45 96.612 34.900 33.595 1.00 47.53 S ATOM 26830 SG CYS L 19 61.149 60.757 19.647 1.00121.75 S ATOM 26849 SG CYS L 22 61.352 59.542 16.086 1.00128.01 S ATOM 26966 SG CYS L 36 59.632 62.873 16.914 1.00126.33 S ATOM 26992 SG CYS L 39 57.972 59.565 17.710 1.00128.84 S ATOM 44266 SG CYS O 88 47.665 155.284 14.816 1.00 89.33 S ATOM 44279 SG CYS O 90 50.590 153.320 13.288 1.00 94.80 S ATOM 44314 SG CYS O 94 50.432 156.637 12.152 1.00 91.39 S ATOM 44336 SG CYS O 97 51.169 156.583 15.568 1.00 87.51 S ATOM 51633 SG CYS U 17 133.962 174.268 100.003 1.00114.39 S ATOM 51657 SG CYS U 20 135.206 171.216 98.284 1.00114.04 S ATOM 51818 SG CYS U 39 132.694 170.927 101.260 1.00117.42 S ATOM 51843 SG CYS U 42 136.314 171.840 101.839 1.00119.11 S ATOM 52195 SG CYS U 86 108.253 206.269 87.514 1.00 98.11 S ATOM 52219 SG CYS U 89 110.918 208.011 85.336 1.00100.39 S ATOM 52423 SG CYS U 114 108.528 205.304 83.873 1.00 92.64 S ATOM 52458 SG CYS U 119 111.342 204.445 86.208 1.00 99.35 S ATOM 52568 SG CYS V 7 62.615 179.146 35.472 1.00 50.98 S ATOM 52592 SG CYS V 10 59.058 180.132 34.361 1.00 45.08 S ATOM 52856 SG CYS V 44 60.812 181.965 37.216 1.00 45.18 S ATOM 52862 SG CYS V 45 61.889 182.428 33.603 1.00 47.61 S ATOM 53990 SG CYS X 19 97.349 156.566 19.652 1.00118.89 S ATOM 54009 SG CYS X 22 97.145 157.782 16.092 1.00126.52 S ATOM 54126 SG CYS X 36 98.866 154.451 16.919 1.00125.84 S ATOM 54152 SG CYS X 39 100.526 157.759 17.716 1.00125.60 S Time building chain proxies: 22.55, per 1000 atoms: 0.42 Number of scatterers: 54330 At special positions: 0 Unit cell: (159.315, 218.139, 148.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 312 16.00 O 10238 8.00 N 9406 7.00 C 34364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 16.60 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 90 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 97 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 88 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 17 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 42 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 20 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 39 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 119 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 114 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 89 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 86 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 22 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 36 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 39 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 19 " Number of angles added : 60 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12796 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 78 sheets defined 39.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.811A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.635A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.660A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.679A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.061A pdb=" N ASP A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.563A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.878A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.556A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 removed outlier: 3.509A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.722A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.975A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.517A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.585A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 3.523A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1281 through 1293 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.927A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.746A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 4.038A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.290A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.524A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.574A pdb=" N ARG B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.661A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.558A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.143A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.700A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.612A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.548A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.159A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.512A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.693A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.568A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.861A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.999A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.961A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.685A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.900A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.555A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.351A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.240A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.523A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 removed outlier: 3.653A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.776A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.701A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.160A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.427A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 4.084A pdb=" N GLU D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.910A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.636A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.583A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.599A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.813A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.607A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.971A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.633A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.275A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 4.114A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.797A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.642A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.773A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.190A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.849A pdb=" N LYS K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 395 through 397 No H-bonds generated for 'chain 'M' and resid 395 through 397' Processing helix chain 'M' and resid 398 through 409 removed outlier: 3.810A pdb=" N GLY M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 508 through 519 Processing helix chain 'M' and resid 520 through 525 Processing helix chain 'M' and resid 538 through 549 removed outlier: 3.635A pdb=" N THR M 543 " --> pdb=" O GLN M 539 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA M 544 " --> pdb=" O ASP M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 556 through 566 removed outlier: 3.661A pdb=" N ASN M 562 " --> pdb=" O GLY M 558 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 566 " --> pdb=" O ASN M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 596 removed outlier: 3.678A pdb=" N LEU M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE M 595 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 616 removed outlier: 4.062A pdb=" N ASP M 614 " --> pdb=" O PRO M 610 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 660 Processing helix chain 'M' and resid 661 through 684 removed outlier: 3.563A pdb=" N THR M 665 " --> pdb=" O GLY M 661 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE M 682 " --> pdb=" O ASN M 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 688 through 693 removed outlier: 3.879A pdb=" N SER M 692 " --> pdb=" O GLY M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 695 through 722 Processing helix chain 'M' and resid 732 through 760 Processing helix chain 'M' and resid 764 through 773 Processing helix chain 'M' and resid 777 through 785 Processing helix chain 'M' and resid 832 through 869 removed outlier: 3.557A pdb=" N PHE M 837 " --> pdb=" O PRO M 833 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA M 855 " --> pdb=" O ALA M 851 " (cutoff:3.500A) Processing helix chain 'M' and resid 890 through 894 Processing helix chain 'M' and resid 914 through 921 removed outlier: 3.509A pdb=" N LYS M 918 " --> pdb=" O LYS M 914 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 934 Processing helix chain 'M' and resid 935 through 945 removed outlier: 3.723A pdb=" N ASN M 945 " --> pdb=" O ASP M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 970 removed outlier: 3.974A pdb=" N GLN M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG M 967 " --> pdb=" O ARG M 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 968 " --> pdb=" O GLU M 964 " (cutoff:3.500A) Processing helix chain 'M' and resid 982 through 994 Processing helix chain 'M' and resid 1005 through 1020 removed outlier: 3.518A pdb=" N VAL M1009 " --> pdb=" O HIS M1005 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL M1010 " --> pdb=" O PRO M1006 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M1018 " --> pdb=" O LYS M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1027 through 1038 Processing helix chain 'M' and resid 1038 through 1049 Processing helix chain 'M' and resid 1050 through 1057 Processing helix chain 'M' and resid 1061 through 1080 Processing helix chain 'M' and resid 1086 through 1100 Proline residue: M1098 - end of helix Processing helix chain 'M' and resid 1120 through 1129 Processing helix chain 'M' and resid 1145 through 1149 Processing helix chain 'M' and resid 1151 through 1153 No H-bonds generated for 'chain 'M' and resid 1151 through 1153' Processing helix chain 'M' and resid 1154 through 1162 Processing helix chain 'M' and resid 1165 through 1169 removed outlier: 3.586A pdb=" N VAL M1169 " --> pdb=" O THR M1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1165 through 1169' Processing helix chain 'M' and resid 1189 through 1199 removed outlier: 3.523A pdb=" N ASN M1194 " --> pdb=" O GLN M1190 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL M1195 " --> pdb=" O GLU M1191 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET M1199 " --> pdb=" O VAL M1195 " (cutoff:3.500A) Processing helix chain 'M' and resid 1217 through 1225 Processing helix chain 'M' and resid 1227 through 1240 Processing helix chain 'M' and resid 1262 through 1267 Processing helix chain 'M' and resid 1281 through 1293 Processing helix chain 'M' and resid 1342 through 1348 removed outlier: 3.928A pdb=" N SER M1348 " --> pdb=" O MET M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1361 through 1369 Processing helix chain 'M' and resid 1370 through 1389 removed outlier: 3.747A pdb=" N LYS M1376 " --> pdb=" O GLU M1372 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP M1389 " --> pdb=" O VAL M1385 " (cutoff:3.500A) Processing helix chain 'M' and resid 1394 through 1406 Processing helix chain 'M' and resid 1478 through 1482 removed outlier: 4.037A pdb=" N TYR M1482 " --> pdb=" O LYS M1479 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 4.290A pdb=" N GLN N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU N 24 " --> pdb=" O ASP N 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 53 removed outlier: 3.524A pdb=" N SER N 46 " --> pdb=" O GLN N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 61 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.573A pdb=" N ARG N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 174 Processing helix chain 'N' and resid 248 through 253 Processing helix chain 'N' and resid 269 through 277 Processing helix chain 'N' and resid 280 through 289 removed outlier: 3.660A pdb=" N ILE N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 310 removed outlier: 4.168A pdb=" N MET N 298 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Proline residue: N 303 - end of helix removed outlier: 3.558A pdb=" N ASP N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL N 310 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 removed outlier: 4.143A pdb=" N ARG N 324 " --> pdb=" O PHE N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 3.702A pdb=" N ARG N 335 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE N 336 " --> pdb=" O LYS N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 378 Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 395 through 426 removed outlier: 3.612A pdb=" N GLY N 406 " --> pdb=" O PHE N 402 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET N 407 " --> pdb=" O LEU N 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS N 421 " --> pdb=" O ILE N 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE N 422 " --> pdb=" O TYR N 418 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG N 425 " --> pdb=" O LYS N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 removed outlier: 3.547A pdb=" N ALA N 434 " --> pdb=" O ASN N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 451 removed outlier: 4.159A pdb=" N ILE N 440 " --> pdb=" O LYS N 436 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 444 " --> pdb=" O ILE N 440 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 447 " --> pdb=" O GLY N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 483 Processing helix chain 'N' and resid 490 through 496 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.512A pdb=" N LEU N 505 " --> pdb=" O HIS N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 548 removed outlier: 3.692A pdb=" N GLU N 546 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP N 548 " --> pdb=" O PHE N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 562 removed outlier: 3.568A pdb=" N ALA N 562 " --> pdb=" O ALA N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 593 removed outlier: 3.861A pdb=" N LEU N 583 " --> pdb=" O ASP N 579 " (cutoff:3.500A) Processing helix chain 'N' and resid 607 through 609 No H-bonds generated for 'chain 'N' and resid 607 through 609' Processing helix chain 'N' and resid 636 through 645 Processing helix chain 'N' and resid 652 through 659 removed outlier: 3.997A pdb=" N LEU N 656 " --> pdb=" O SER N 652 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL N 657 " --> pdb=" O TRP N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 672 removed outlier: 3.961A pdb=" N THR N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 678 through 684 removed outlier: 3.684A pdb=" N LEU N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU N 684 " --> pdb=" O ASP N 680 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 704 Processing helix chain 'N' and resid 705 through 710 removed outlier: 3.900A pdb=" N ILE N 710 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 718 through 732 removed outlier: 3.555A pdb=" N ALA N 727 " --> pdb=" O THR N 723 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS N 730 " --> pdb=" O SER N 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 762 through 767 removed outlier: 4.350A pdb=" N TYR N 766 " --> pdb=" O ARG N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 803 Processing helix chain 'N' and resid 969 through 972 Processing helix chain 'N' and resid 977 through 994 removed outlier: 4.240A pdb=" N LEU N 981 " --> pdb=" O THR N 977 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1017 removed outlier: 3.523A pdb=" N ASP N1017 " --> pdb=" O ASN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1054 through 1061 removed outlier: 3.652A pdb=" N LYS N1058 " --> pdb=" O MET N1054 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 40 removed outlier: 3.776A pdb=" N ILE O 39 " --> pdb=" O ARG O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 removed outlier: 3.701A pdb=" N LEU O 68 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU O 70 " --> pdb=" O HIS O 66 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE O 71 " --> pdb=" O ARG O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 118 through 120 No H-bonds generated for 'chain 'O' and resid 118 through 120' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 240 through 271 removed outlier: 4.159A pdb=" N VAL O 245 " --> pdb=" O PRO O 241 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU O 246 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 removed outlier: 4.427A pdb=" N THR P 28 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 29' Processing helix chain 'P' and resid 33 through 51 Processing helix chain 'P' and resid 58 through 71 Processing helix chain 'P' and resid 76 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 115 Processing helix chain 'P' and resid 115 through 122 removed outlier: 4.083A pdb=" N GLU P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY P 120 " --> pdb=" O PRO P 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG P 121 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.911A pdb=" N ASP P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 removed outlier: 3.637A pdb=" N TYR Q 8 " --> pdb=" O GLU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.583A pdb=" N LEU Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Q 34 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 34' Processing helix chain 'Q' and resid 36 through 45 removed outlier: 3.598A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 98 removed outlier: 3.813A pdb=" N GLU Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 121 removed outlier: 3.614A pdb=" N GLN Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 136 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 58 through 75 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 21 through 34 removed outlier: 3.971A pdb=" N THR S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR S 32 " --> pdb=" O GLN S 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 75 removed outlier: 3.634A pdb=" N SER U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 4.276A pdb=" N ASP U 106 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 26 removed outlier: 4.114A pdb=" N GLU V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 39 removed outlier: 3.796A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 51 removed outlier: 3.642A pdb=" N MET V 48 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.773A pdb=" N SER W 9 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.190A pdb=" N ILE W 45 " --> pdb=" O THR W 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN W 49 " --> pdb=" O ILE W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 68 Processing helix chain 'W' and resid 82 through 115 removed outlier: 3.849A pdb=" N LYS W 110 " --> pdb=" O ARG W 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.124A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.520A pdb=" N CYS A 602 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AA8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.917A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1320 through 1322 removed outlier: 3.757A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.613A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.532A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.735A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.500A pdb=" N PHE B 208 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 233 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC2, first strand: chain 'B' and resid 572 through 573 removed outlier: 5.969A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC6, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.980A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 827 through 828 removed outlier: 4.814A pdb=" N CYS B 837 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 891 " --> pdb=" O CYS B 837 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 839 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.625A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.771A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.882A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD4, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.247A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.065A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.871A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 92 removed outlier: 7.305A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AD9, first strand: chain 'H' and resid 101 through 102 removed outlier: 4.189A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE3, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AE4, first strand: chain 'M' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR M 368 " --> pdb=" O LEU M 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL M 378 " --> pdb=" O ARG M 475 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU M 477 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL M 380 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 389 through 393 removed outlier: 4.125A pdb=" N TYR M 418 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS M 449 " --> pdb=" O ALA M 416 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA M 416 " --> pdb=" O HIS M 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 554 through 555 Processing sheet with id=AE7, first strand: chain 'M' and resid 602 through 605 removed outlier: 3.518A pdb=" N CYS M 602 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL M 629 " --> pdb=" O ILE M 636 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 789 through 790 Processing sheet with id=AE9, first strand: chain 'M' and resid 872 through 873 Processing sheet with id=AF1, first strand: chain 'M' and resid 902 through 905 Processing sheet with id=AF2, first strand: chain 'M' and resid 1307 through 1310 removed outlier: 3.917A pdb=" N ILE M1335 " --> pdb=" O HIS M1310 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR M1358 " --> pdb=" O THR M1140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU M1255 " --> pdb=" O LEU M1216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN M1172 " --> pdb=" O GLU M1215 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR U 54 " --> pdb=" O ILE M1175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 1320 through 1322 removed outlier: 3.757A pdb=" N LYS M1329 " --> pdb=" O ILE M1321 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY S 57 " --> pdb=" O LEU M1475 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU M1473 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.614A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE S 54 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS S 71 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE S 75 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL S 48 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE S 77 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE S 46 " --> pdb=" O PHE S 77 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 65 through 67 removed outlier: 3.614A pdb=" N TYR N 84 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR N 84 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE N 133 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU N 86 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR N 131 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE N 88 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR N 129 " --> pdb=" O PHE N 88 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN N 90 " --> pdb=" O ASP N 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL N 126 " --> pdb=" O PHE N 148 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE N 148 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE N 128 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS N 146 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS N 130 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS N 144 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL N 132 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR N 142 " --> pdb=" O VAL N 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.532A pdb=" N SER N 106 " --> pdb=" O HIS N 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 185 through 187 Processing sheet with id=AG1, first strand: chain 'N' and resid 391 through 394 removed outlier: 3.735A pdb=" N ALA N 196 " --> pdb=" O ARG N 484 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 206 through 209 removed outlier: 3.532A pdb=" N TYR N 217 " --> pdb=" O MET N 239 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE N 235 " --> pdb=" O CYS N 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER N 233 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP N 236 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG4, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG5, first strand: chain 'N' and resid 572 through 573 removed outlier: 5.969A pdb=" N LYS N 566 " --> pdb=" O ILE N 612 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE N 614 " --> pdb=" O LYS N 566 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE N 568 " --> pdb=" O ILE N 614 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.782A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL N 907 " --> pdb=" O LYS X 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 759 through 760 Processing sheet with id=AG9, first strand: chain 'N' and resid 1025 through 1026 removed outlier: 6.981A pdb=" N VAL N 794 " --> pdb=" O GLY N 946 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN N 948 " --> pdb=" O VAL N 794 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET N 796 " --> pdb=" O GLN N 948 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE N 965 " --> pdb=" O ILE N 779 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 967 " --> pdb=" O ALA N 781 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE N1042 " --> pdb=" O ILE N 782 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 827 through 828 removed outlier: 4.815A pdb=" N CYS N 837 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP N 891 " --> pdb=" O CYS N 837 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY N 839 " --> pdb=" O ASP N 891 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 865 through 867 removed outlier: 3.625A pdb=" N ILE N 866 " --> pdb=" O THR N 894 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR N 894 " --> pdb=" O ILE N 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 956 through 957 Processing sheet with id=AH4, first strand: chain 'O' and resid 8 through 14 removed outlier: 6.772A pdb=" N LYS O 20 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU O 14 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASN O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN O 232 " --> pdb=" O VAL O 182 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL O 182 " --> pdb=" O ASN O 232 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU O 234 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 121 through 122 removed outlier: 6.883A pdb=" N GLU O 158 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN O 55 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG O 160 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS O 166 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE O 47 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY O 168 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE O 45 " --> pdb=" O GLY O 168 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 113 through 116 Processing sheet with id=AH7, first strand: chain 'Q' and resid 26 through 27 removed outlier: 4.247A pdb=" N ALA Q 63 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL Q 60 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Q 62 " --> pdb=" O MET Q 72 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG Q 101 " --> pdb=" O GLN Q 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Q 128 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 81 through 82 removed outlier: 4.066A pdb=" N VAL Q 82 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 147 through 151 removed outlier: 3.873A pdb=" N GLU Q 147 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL Q 190 " --> pdb=" O MET Q 151 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 83 through 92 removed outlier: 7.306A pdb=" N PHE S 98 " --> pdb=" O THR S 90 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER S 105 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA S 159 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER S 162 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE S 147 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU S 83 " --> pdb=" O ILE S 147 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 117 through 118 Processing sheet with id=AI3, first strand: chain 'T' and resid 101 through 102 removed outlier: 4.190A pdb=" N ARG T 111 " --> pdb=" O ASP T 102 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU T 122 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU T 41 " --> pdb=" O LEU T 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU T 31 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL T 12 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE T 60 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU T 7 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU T 58 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE T 9 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE T 56 " --> pdb=" O ILE T 9 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL T 96 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER T 117 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG T 98 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 26 through 28 Processing sheet with id=AI5, first strand: chain 'U' and resid 80 through 81 Processing sheet with id=AI6, first strand: chain 'W' and resid 21 through 23 2235 hydrogen bonds defined for protein. 6285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.32 Time building geometry restraints manager: 18.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 18152 1.35 - 1.46: 11834 1.46 - 1.58: 24870 1.58 - 1.70: 0 1.70 - 1.82: 496 Bond restraints: 55352 Sorted by residual: bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 55347 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 1632 107.03 - 113.77: 30766 113.77 - 120.51: 21709 120.51 - 127.25: 20119 127.25 - 134.00: 560 Bond angle restraints: 74786 Sorted by residual: angle pdb=" C ILE B 972 " pdb=" CA ILE B 972 " pdb=" CB ILE B 972 " ideal model delta sigma weight residual 113.70 110.55 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" C ILE N 972 " pdb=" CA ILE N 972 " pdb=" CB ILE N 972 " ideal model delta sigma weight residual 113.70 110.57 3.13 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C ALA B 971 " pdb=" N ILE B 972 " pdb=" CA ILE B 972 " ideal model delta sigma weight residual 120.43 123.23 -2.80 9.60e-01 1.09e+00 8.48e+00 angle pdb=" C ALA N 971 " pdb=" N ILE N 972 " pdb=" CA ILE N 972 " ideal model delta sigma weight residual 120.43 123.16 -2.73 9.60e-01 1.09e+00 8.11e+00 angle pdb=" C ASN N 227 " pdb=" CA ASN N 227 " pdb=" CB ASN N 227 " ideal model delta sigma weight residual 110.42 114.61 -4.19 1.99e+00 2.53e-01 4.44e+00 ... (remaining 74781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 30773 17.89 - 35.78: 2522 35.78 - 53.67: 447 53.67 - 71.57: 102 71.57 - 89.46: 76 Dihedral angle restraints: 33920 sinusoidal: 14154 harmonic: 19766 Sorted by residual: dihedral pdb=" CA GLU B 226 " pdb=" C GLU B 226 " pdb=" N ASN B 227 " pdb=" CA ASN B 227 " ideal model delta harmonic sigma weight residual -180.00 -135.94 -44.06 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA GLU N 226 " pdb=" C GLU N 226 " pdb=" N ASN N 227 " pdb=" CA ASN N 227 " ideal model delta harmonic sigma weight residual 180.00 -135.97 -44.03 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA CYS O 90 " pdb=" C CYS O 90 " pdb=" N GLU O 91 " pdb=" CA GLU O 91 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 33917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5813 0.030 - 0.060: 1531 0.060 - 0.090: 437 0.090 - 0.120: 524 0.120 - 0.150: 57 Chirality restraints: 8362 Sorted by residual: chirality pdb=" CA ILE M 596 " pdb=" N ILE M 596 " pdb=" C ILE M 596 " pdb=" CB ILE M 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE V 3 " pdb=" N ILE V 3 " pdb=" C ILE V 3 " pdb=" CB ILE V 3 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE A 798 " pdb=" N ILE A 798 " pdb=" C ILE A 798 " pdb=" CB ILE A 798 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 8359 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 395 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO M 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO M 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 521 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 522 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " -0.020 5.00e-02 4.00e+02 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 510 2.57 - 3.16: 46299 3.16 - 3.74: 85542 3.74 - 4.32: 120471 4.32 - 4.90: 200227 Nonbonded interactions: 453049 Sorted by model distance: nonbonded pdb=" OD1 ASN M 372 " pdb=" OH TYR N 788 " model vdw 1.993 2.440 nonbonded pdb=" OD1 ASN A 372 " pdb=" OH TYR B 788 " model vdw 1.993 2.440 nonbonded pdb=" OH TYR A 763 " pdb=" OD2 ASP H 23 " model vdw 2.019 2.440 nonbonded pdb=" OH TYR M 763 " pdb=" OD2 ASP T 23 " model vdw 2.020 2.440 nonbonded pdb=" OG SER M 867 " pdb=" OG1 THR M1415 " model vdw 2.075 2.440 ... (remaining 453044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 312 5.16 5 C 34364 2.51 5 N 9406 2.21 5 O 10238 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.910 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.340 Process input model: 118.090 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 55352 Z= 0.113 Angle : 0.385 5.156 74786 Z= 0.212 Chirality : 0.039 0.150 8362 Planarity : 0.002 0.058 9702 Dihedral : 14.069 89.457 21124 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 6690 helix: 2.06 (0.12), residues: 2164 sheet: 0.25 (0.17), residues: 974 loop : 0.26 (0.11), residues: 3552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1802 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1802 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1802 average time/residue: 0.5578 time to fit residues: 1627.9117 Evaluate side-chains 840 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 10.0000 chunk 503 optimal weight: 0.1980 chunk 279 optimal weight: 0.0570 chunk 171 optimal weight: 0.8980 chunk 339 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 520 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 316 optimal weight: 0.9980 chunk 387 optimal weight: 20.0000 chunk 602 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 825 ASN A 913 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN B 460 HIS B 518 HIS B 593 GLN B 631 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN C 32 ASN C 265 HIS ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS I 84 HIS I 118 HIS ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 809 HIS M 913 ASN M1077 ASN N 52 GLN N 518 HIS N 631 GLN ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1053 HIS O 32 ASN O 51 GLN O 265 HIS ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 HIS U 84 HIS U 118 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 55352 Z= 0.235 Angle : 0.646 10.416 74786 Z= 0.335 Chirality : 0.045 0.196 8362 Planarity : 0.006 0.115 9702 Dihedral : 3.521 42.528 7396 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 6690 helix: 1.19 (0.11), residues: 2338 sheet: -0.07 (0.16), residues: 1012 loop : 0.02 (0.11), residues: 3340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 989 time to evaluate : 5.150 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 outliers start: 160 outliers final: 74 residues processed: 1097 average time/residue: 0.5350 time to fit residues: 986.0721 Evaluate side-chains 785 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 711 time to evaluate : 4.819 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.3894 time to fit residues: 60.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 9.9990 chunk 187 optimal weight: 0.0030 chunk 501 optimal weight: 9.9990 chunk 410 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 604 optimal weight: 6.9990 chunk 652 optimal weight: 0.8980 chunk 537 optimal weight: 10.0000 chunk 599 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 484 optimal weight: 4.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 780 ASN A1077 ASN A1078 GLN B 52 GLN B 344 GLN ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 HIS C 265 HIS D 38 HIS D 47 GLN E 132 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN M 504 HIS M 780 ASN M1077 ASN M1078 GLN M1101 GLN ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 55352 Z= 0.283 Angle : 0.648 9.131 74786 Z= 0.332 Chirality : 0.046 0.274 8362 Planarity : 0.005 0.104 9702 Dihedral : 3.893 44.416 7396 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 6690 helix: 0.98 (0.11), residues: 2352 sheet: -0.20 (0.15), residues: 1024 loop : -0.20 (0.11), residues: 3314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 788 time to evaluate : 4.880 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 outliers start: 138 outliers final: 60 residues processed: 873 average time/residue: 0.5078 time to fit residues: 747.1204 Evaluate side-chains 703 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 643 time to evaluate : 4.824 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3970 time to fit residues: 50.8767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 0.0020 chunk 454 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 606 optimal weight: 3.9990 chunk 641 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 574 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 601 ASN A 989 ASN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 699 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 471 ASN ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 725 GLN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 GLN ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 ASN ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN W 69 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.129 55352 Z= 0.266 Angle : 0.621 11.069 74786 Z= 0.318 Chirality : 0.045 0.270 8362 Planarity : 0.005 0.100 9702 Dihedral : 4.022 44.028 7396 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.10), residues: 6690 helix: 0.86 (0.11), residues: 2354 sheet: -0.45 (0.15), residues: 1080 loop : -0.29 (0.11), residues: 3256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 726 time to evaluate : 5.897 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 outliers start: 139 outliers final: 67 residues processed: 811 average time/residue: 0.5155 time to fit residues: 710.2253 Evaluate side-chains 690 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 623 time to evaluate : 4.861 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.3990 time to fit residues: 56.5824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 0.8980 chunk 364 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 477 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 547 optimal weight: 6.9990 chunk 443 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 327 optimal weight: 1.9990 chunk 576 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 ASN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN E 138 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 410 ASN ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1163 HIS ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 254 GLN N 344 GLN N 699 HIS N 930 GLN O 51 GLN ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN W 69 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.117 55352 Z= 0.202 Angle : 0.592 11.842 74786 Z= 0.299 Chirality : 0.044 0.302 8362 Planarity : 0.005 0.102 9702 Dihedral : 3.950 42.181 7396 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.10), residues: 6690 helix: 0.95 (0.11), residues: 2344 sheet: -0.50 (0.15), residues: 1076 loop : -0.22 (0.11), residues: 3270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 731 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 35 residues processed: 797 average time/residue: 0.5131 time to fit residues: 695.3959 Evaluate side-chains 665 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 630 time to evaluate : 4.901 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3912 time to fit residues: 32.4859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 5.9990 chunk 577 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 642 optimal weight: 0.6980 chunk 533 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 337 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN A1101 GLN A1303 GLN A1332 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 GLN ** M 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.133 55352 Z= 0.383 Angle : 0.699 10.039 74786 Z= 0.359 Chirality : 0.048 0.316 8362 Planarity : 0.006 0.115 9702 Dihedral : 4.381 43.099 7396 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.20 (0.10), residues: 6690 helix: 0.65 (0.11), residues: 2342 sheet: -0.72 (0.15), residues: 1050 loop : -0.40 (0.11), residues: 3298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 681 time to evaluate : 4.909 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 outliers start: 132 outliers final: 74 residues processed: 765 average time/residue: 0.5138 time to fit residues: 667.7083 Evaluate side-chains 684 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 610 time to evaluate : 4.948 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.4027 time to fit residues: 62.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 366 optimal weight: 0.0170 chunk 469 optimal weight: 0.8980 chunk 363 optimal weight: 5.9990 chunk 540 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 chunk 639 optimal weight: 0.9980 chunk 400 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 989 ASN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B1053 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN I 121 HIS ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 GLN ** M 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1163 HIS M1332 GLN ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.206 55352 Z= 0.226 Angle : 0.634 15.002 74786 Z= 0.323 Chirality : 0.045 0.310 8362 Planarity : 0.005 0.115 9702 Dihedral : 4.228 41.806 7396 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.06 (0.10), residues: 6690 helix: 0.82 (0.11), residues: 2340 sheet: -0.68 (0.15), residues: 1068 loop : -0.33 (0.11), residues: 3282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 718 time to evaluate : 4.866 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 outliers start: 81 outliers final: 29 residues processed: 759 average time/residue: 0.5190 time to fit residues: 666.1033 Evaluate side-chains 636 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 607 time to evaluate : 4.884 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4011 time to fit residues: 28.3838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 chunk 123 optimal weight: 0.0970 chunk 406 optimal weight: 0.7980 chunk 436 optimal weight: 0.8980 chunk 316 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 503 optimal weight: 0.7980 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1291 ASN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 GLN M 673 GLN M 757 GLN M 913 ASN ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 GLN ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS W 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.144 55352 Z= 0.239 Angle : 0.653 13.331 74786 Z= 0.331 Chirality : 0.046 0.328 8362 Planarity : 0.005 0.135 9702 Dihedral : 4.268 41.495 7396 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.07 (0.10), residues: 6690 helix: 0.77 (0.11), residues: 2342 sheet: -0.62 (0.15), residues: 1018 loop : -0.35 (0.11), residues: 3330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 658 time to evaluate : 5.263 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: 43 outliers final: 18 residues processed: 683 average time/residue: 0.5181 time to fit residues: 601.0554 Evaluate side-chains 618 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 600 time to evaluate : 4.830 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4114 time to fit residues: 20.3904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 8.9990 chunk 613 optimal weight: 9.9990 chunk 559 optimal weight: 4.9990 chunk 596 optimal weight: 9.9990 chunk 612 optimal weight: 0.8980 chunk 358 optimal weight: 4.9990 chunk 259 optimal weight: 0.5980 chunk 468 optimal weight: 10.0000 chunk 183 optimal weight: 0.2980 chunk 538 optimal weight: 1.9990 chunk 564 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 673 GLN M 765 ASN ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.263 55352 Z= 0.264 Angle : 0.671 15.797 74786 Z= 0.344 Chirality : 0.046 0.305 8362 Planarity : 0.005 0.150 9702 Dihedral : 4.332 41.866 7396 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.11 (0.10), residues: 6690 helix: 0.74 (0.11), residues: 2328 sheet: -0.62 (0.15), residues: 1008 loop : -0.39 (0.11), residues: 3354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 645 time to evaluate : 4.915 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 outliers start: 43 outliers final: 25 residues processed: 665 average time/residue: 0.5228 time to fit residues: 591.2318 Evaluate side-chains 625 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 600 time to evaluate : 4.856 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4072 time to fit residues: 25.6853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 0.0060 chunk 391 optimal weight: 0.9990 chunk 630 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 438 optimal weight: 5.9990 chunk 661 optimal weight: 30.0000 chunk 608 optimal weight: 1.9990 chunk 526 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS W 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.534 55352 Z= 0.332 Angle : 0.765 73.900 74786 Z= 0.382 Chirality : 0.046 0.317 8362 Planarity : 0.006 0.171 9702 Dihedral : 4.365 41.931 7396 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.12 (0.10), residues: 6690 helix: 0.75 (0.11), residues: 2328 sheet: -0.62 (0.15), residues: 996 loop : -0.40 (0.11), residues: 3366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 623 time to evaluate : 4.857 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: 26 outliers final: 18 residues processed: 638 average time/residue: 0.5143 time to fit residues: 560.3089 Evaluate side-chains 621 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 603 time to evaluate : 4.856 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4153 time to fit residues: 20.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 561 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 485 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 527 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 541 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 HIS W 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.132534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.105998 restraints weight = 128669.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105759 restraints weight = 82531.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106891 restraints weight = 75176.801| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.184 55352 Z= 0.239 Angle : 0.676 18.487 74786 Z= 0.347 Chirality : 0.046 0.309 8362 Planarity : 0.005 0.149 9702 Dihedral : 4.329 42.203 7396 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.09 (0.10), residues: 6690 helix: 0.79 (0.11), residues: 2320 sheet: -0.62 (0.15), residues: 1020 loop : -0.39 (0.11), residues: 3350 =============================================================================== Job complete usr+sys time: 11831.15 seconds wall clock time: 209 minutes 22.38 seconds (12562.38 seconds total)