Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 11:45:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/10_2023/7ozp_13131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/10_2023/7ozp_13131.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/7ozp_13131/10_2023/7ozp_13131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/10_2023/7ozp_13131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/10_2023/7ozp_13131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/10_2023/7ozp_13131.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.921 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 312 5.16 5 C 34364 2.51 5 N 9406 2.21 5 O 10238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F ASP 112": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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-1.21rc1-5097/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: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} 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 88 119.305 60.478 14.511 1.00 88.48 S ATOM 17119 SG CYS C 90 116.492 62.194 12.536 1.00 96.81 S ATOM 17154 SG CYS C 94 116.874 58.802 11.711 1.00 89.88 S ATOM 17176 SG CYS C 97 115.785 59.110 15.021 1.00 85.73 S ATOM 24473 SG CYS I 17 25.152 44.936 91.935 1.00 97.63 S ATOM 24497 SG CYS I 20 23.998 47.782 89.837 1.00101.80 S ATOM 24658 SG CYS I 39 26.162 48.418 93.021 1.00101.17 S ATOM 24683 SG CYS I 42 22.531 47.402 93.297 1.00102.57 S ATOM 25035 SG CYS I 86 53.095 13.145 84.921 1.00 81.20 S ATOM 25059 SG CYS I 89 50.741 11.122 82.631 1.00 81.91 S ATOM 25263 SG CYS I 114 53.180 13.804 81.203 1.00 72.52 S ATOM 25298 SG CYS I 119 50.104 14.726 83.149 1.00 76.54 S ATOM 25408 SG CYS J 7 103.144 37.532 35.444 1.00 36.75 S ATOM 25432 SG CYS J 10 106.829 36.631 34.766 1.00 32.02 S ATOM 25696 SG CYS J 44 104.876 34.936 37.576 1.00 30.26 S ATOM 25702 SG CYS J 45 104.176 34.153 33.929 1.00 37.06 S ATOM 26830 SG CYS L 19 69.481 57.081 14.225 1.00 97.39 S ATOM 26849 SG CYS L 22 70.139 55.504 10.860 1.00101.71 S ATOM 26966 SG CYS L 36 68.216 58.809 11.115 1.00100.08 S ATOM 26992 SG CYS L 39 66.601 55.526 12.092 1.00102.43 S ATOM 44266 SG CYS O 88 42.452 161.747 14.515 1.00 89.06 S ATOM 44279 SG CYS O 90 45.265 160.032 12.539 1.00 92.99 S ATOM 44314 SG CYS O 94 44.882 163.424 11.715 1.00 90.40 S ATOM 44336 SG CYS O 97 45.972 163.115 15.025 1.00 88.12 S ATOM 51633 SG CYS U 17 136.623 177.278 91.921 1.00100.22 S ATOM 51657 SG CYS U 20 137.776 174.433 89.822 1.00104.52 S ATOM 51818 SG CYS U 39 135.612 173.795 93.007 1.00104.69 S ATOM 51843 SG CYS U 42 139.244 174.812 93.281 1.00104.98 S ATOM 52195 SG CYS U 86 108.675 209.069 84.921 1.00 84.51 S ATOM 52219 SG CYS U 89 111.029 211.092 82.631 1.00 85.52 S ATOM 52423 SG CYS U 114 108.590 208.410 81.203 1.00 73.90 S ATOM 52458 SG CYS U 119 111.666 207.488 83.148 1.00 79.57 S ATOM 52568 SG CYS V 7 58.616 184.689 35.451 1.00 36.72 S ATOM 52592 SG CYS V 10 54.931 185.590 34.774 1.00 31.26 S ATOM 52856 SG CYS V 44 56.885 187.284 37.583 1.00 31.67 S ATOM 52862 SG CYS V 45 57.583 188.068 33.936 1.00 36.98 S ATOM 53990 SG CYS X 19 92.276 165.148 14.218 1.00 94.65 S ATOM 54009 SG CYS X 22 91.617 166.726 10.854 1.00 98.35 S ATOM 54126 SG CYS X 36 93.540 163.420 11.108 1.00 96.68 S ATOM 54152 SG CYS X 39 95.155 166.703 12.085 1.00 98.43 S Time building chain proxies: 20.23, per 1000 atoms: 0.37 Number of scatterers: 54330 At special positions: 0 Unit cell: (162.583, 223.041, 142.975, 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: 16.13 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " 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 86 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 89 " 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: 235 helices and 78 sheets defined 39.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 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: 3.812A 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: 3.638A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.655A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.680A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.055A pdb=" N ASP A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.535A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.867A 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 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.507A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.657A 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 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.720A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.972A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.505A 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 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.521A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.588A 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: 3.520A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.493A 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 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.937A 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: 3.736A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.265A 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 1476 through 1481 removed outlier: 3.617A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.304A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.520A 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: 3.580A 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: 3.664A 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: 3.717A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.560A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.146A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.702A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.506A pdb=" N ARG B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.728A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.554A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.165A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.509A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.694A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.630A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.862A 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: 3.991A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.949A 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: 4.311A 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: 3.904A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.550A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.348A 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: 4.237A 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: 3.650A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.787A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.702A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.157A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 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: 3.638A 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: 3.965A pdb=" N GLU D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.917A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.638A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.584A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.540A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.814A 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: 3.613A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.922A 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: 3.623A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.662A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.293A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 4.141A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.784A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.649A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.758A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.193A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.852A pdb=" N LYS K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 3.783A 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: 3.811A 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: 3.638A pdb=" N THR M 543 " --> pdb=" O GLN M 539 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA M 544 " --> pdb=" O ASP M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 556 through 566 removed outlier: 3.655A pdb=" N ASN M 562 " --> pdb=" O GLY M 558 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE M 566 " --> pdb=" O ASN M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 596 removed outlier: 3.680A pdb=" N LEU M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE M 595 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 616 removed outlier: 4.054A pdb=" N ASP M 614 " --> pdb=" O PRO M 610 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 641 through 646 Processing helix chain 'M' and resid 651 through 660 Processing helix chain 'M' and resid 661 through 684 removed outlier: 3.534A pdb=" N THR M 665 " --> pdb=" O GLY M 661 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE M 682 " --> pdb=" O ASN M 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 688 through 693 removed outlier: 3.868A 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 786 Processing helix chain 'M' and resid 832 through 869 removed outlier: 3.507A pdb=" N PHE M 837 " --> pdb=" O PRO M 833 " (cutoff:3.500A) removed outlier: 3.657A 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 Processing helix chain 'M' and resid 926 through 934 Processing helix chain 'M' and resid 935 through 945 removed outlier: 3.719A pdb=" N ASN M 945 " --> pdb=" O ASP M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 970 removed outlier: 3.973A pdb=" N GLN M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG M 967 " --> pdb=" O ARG M 963 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL M 968 " --> pdb=" O GLU M 964 " (cutoff:3.500A) Processing helix chain 'M' and resid 982 through 995 Processing helix chain 'M' and resid 1005 through 1020 removed outlier: 3.520A 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: 3.588A 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: 3.520A pdb=" N ASN M1194 " --> pdb=" O GLN M1190 " (cutoff:3.500A) removed outlier: 4.436A 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 1295 Processing helix chain 'M' and resid 1342 through 1348 removed outlier: 3.937A 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: 3.736A pdb=" N LYS M1376 " --> pdb=" O GLU M1372 " (cutoff:3.500A) removed outlier: 4.266A 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 1476 through 1481 removed outlier: 3.617A pdb=" N CYS M1480 " --> pdb=" O ASP M1476 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 4.304A pdb=" N GLN N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU N 24 " --> pdb=" O ASP N 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 53 removed outlier: 3.520A 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: 3.580A 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: 3.664A pdb=" N ILE N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 310 removed outlier: 4.169A pdb=" N MET N 298 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Proline residue: N 303 - end of helix removed outlier: 3.560A pdb=" N ASP N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL N 310 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 removed outlier: 4.146A pdb=" N ARG N 324 " --> pdb=" O PHE N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 3.701A pdb=" N ARG N 335 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.507A pdb=" N ARG N 405 " --> pdb=" O ALA N 401 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY N 406 " --> pdb=" O PHE N 402 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.728A 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: 3.553A pdb=" N ALA N 434 " --> pdb=" O ASN N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 451 removed outlier: 4.165A pdb=" N ILE N 440 " --> pdb=" O LYS N 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU N 444 " --> pdb=" O ILE N 440 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.508A pdb=" N LEU N 505 " --> pdb=" O HIS N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 548 removed outlier: 3.694A pdb=" N GLU N 546 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP N 548 " --> pdb=" O PHE N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 562 removed outlier: 3.630A pdb=" N ALA N 562 " --> pdb=" O ALA N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 593 removed outlier: 3.863A 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: 3.991A pdb=" N LEU N 656 " --> pdb=" O SER N 652 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 657 " --> pdb=" O TRP N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 672 removed outlier: 3.948A pdb=" N THR N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 678 through 684 removed outlier: 3.685A pdb=" N LEU N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) removed outlier: 4.311A 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: 3.904A pdb=" N ILE N 710 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 718 through 732 removed outlier: 3.549A pdb=" N ALA N 727 " --> pdb=" O THR N 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS N 730 " --> pdb=" O SER N 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 762 through 767 removed outlier: 4.347A 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: 4.237A pdb=" N LEU N 981 " --> pdb=" O THR N 977 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1017 removed outlier: 3.524A pdb=" N ASP N1017 " --> pdb=" O ASN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1054 through 1061 removed outlier: 3.651A pdb=" N LYS N1058 " --> pdb=" O MET N1054 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 40 removed outlier: 3.786A pdb=" N ILE O 39 " --> pdb=" O ARG O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 removed outlier: 3.703A pdb=" N LEU O 68 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU O 70 " --> pdb=" O HIS O 66 " (cutoff:3.500A) removed outlier: 3.769A 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: 4.158A pdb=" N VAL O 245 " --> pdb=" O PRO O 241 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU O 246 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 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: 3.638A 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: 3.966A pdb=" N GLU P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY P 120 " --> pdb=" O PRO P 116 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG P 121 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.917A pdb=" N ASP P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 removed outlier: 3.638A pdb=" N TYR Q 8 " --> pdb=" O GLU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.585A pdb=" N LEU Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.599A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 98 removed outlier: 3.815A pdb=" N GLU Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 121 removed outlier: 3.613A pdb=" N GLN Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.623A pdb=" N THR S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR S 32 " --> pdb=" O GLN S 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 75 removed outlier: 3.663A pdb=" N SER U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 4.293A pdb=" N ASP U 106 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 26 removed outlier: 4.141A pdb=" N GLU V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 39 removed outlier: 3.784A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 51 removed outlier: 3.648A pdb=" N MET V 48 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.759A pdb=" N SER W 9 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.194A pdb=" N ILE W 45 " --> pdb=" O THR W 41 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.852A pdb=" N LYS W 110 " --> pdb=" O ARG W 106 " (cutoff:3.500A) removed outlier: 3.783A 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: 6.970A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.933A 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: 4.125A 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: 6.868A 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: 3.519A pdb=" N CYS A 602 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.023A 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: 3.921A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.714A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.067A 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: 3.758A 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: 3.618A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.330A 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: 3.618A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.835A 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: 7.441A 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: 3.614A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.972A 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: 5.297A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.305A 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: 7.965A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.198A 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: 3.528A 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: 3.746A 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: 3.532A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.523A 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: 5.973A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.846A 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: 3.784A 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: 3.809A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.325A 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: 3.784A 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: 3.809A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.134A 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: 6.983A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.360A 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: 4.840A pdb=" N CYS B 837 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP B 891 " --> pdb=" O CYS B 837 " (cutoff:3.500A) removed outlier: 6.802A 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: 3.640A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.497A 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: 6.759A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.374A 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: 6.878A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.850A 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: 4.246A 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: 3.597A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.653A 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: 4.056A 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: 3.873A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.708A 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: 7.302A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.763A 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: 4.190A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.652A 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: 6.971A pdb=" N LEU M 477 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 5.933A 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: 4.126A pdb=" N TYR M 418 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.377A 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: 3.519A pdb=" N CYS M 602 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 7.023A 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: 3.921A pdb=" N ILE M1335 " --> pdb=" O HIS M1310 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.713A pdb=" N ASN M1172 " --> pdb=" O GLU M1215 " (cutoff:3.500A) removed outlier: 4.067A 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: 3.758A 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: 3.618A 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: 3.753A pdb=" N GLY S 57 " --> pdb=" O LEU M1475 " (cutoff:3.500A) removed outlier: 5.329A 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: 3.618A 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: 5.140A pdb=" N ILE S 54 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS S 71 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE S 75 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 5.835A 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: 7.442A 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: 3.613A pdb=" N TYR N 84 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR N 84 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE N 133 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU N 86 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 7.248A 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: 6.616A pdb=" N THR N 129 " --> pdb=" O PHE N 88 " (cutoff:3.500A) removed outlier: 3.972A 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: 7.815A pdb=" N ILE N 128 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 7.305A 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: 8.264A 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: 3.529A 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: 3.745A 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: 3.594A pdb=" N ILE N 235 " --> pdb=" O CYS N 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER N 233 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 3.960A 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: 5.972A pdb=" N LYS N 566 " --> pdb=" O ILE N 612 " (cutoff:3.500A) removed outlier: 7.235A 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: 3.783A 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: 3.809A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.324A 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: 3.783A 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: 3.809A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) removed outlier: 5.134A 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: 6.983A 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: 6.630A pdb=" N MET N 796 " --> pdb=" O GLN N 948 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE N 965 " --> pdb=" O ILE N 779 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE N 967 " --> pdb=" O ALA N 781 " (cutoff:3.500A) removed outlier: 4.358A 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: 4.840A pdb=" N CYS N 837 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP N 891 " --> pdb=" O CYS N 837 " (cutoff:3.500A) removed outlier: 6.802A 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: 3.639A pdb=" N ILE N 866 " --> pdb=" O THR N 894 " (cutoff:3.500A) removed outlier: 7.499A 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: 6.758A pdb=" N LYS O 20 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU O 14 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN O 232 " --> pdb=" O VAL O 182 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL O 182 " --> pdb=" O ASN O 232 " (cutoff:3.500A) removed outlier: 5.375A 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: 6.878A pdb=" N GLU O 158 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN O 55 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG O 160 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS O 166 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE O 47 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY O 168 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.849A 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: 4.246A pdb=" N ALA Q 63 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.870A 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: 3.597A pdb=" N VAL Q 62 " --> pdb=" O MET Q 72 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG Q 101 " --> pdb=" O GLN Q 71 " (cutoff:3.500A) removed outlier: 3.688A 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: 4.056A 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: 3.874A pdb=" N GLU Q 147 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.709A 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: 7.302A pdb=" N PHE S 98 " --> pdb=" O THR S 90 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER S 105 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA S 159 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER S 162 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE S 147 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 3.763A 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: 5.650A pdb=" N LEU T 122 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.571A 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: 5.869A pdb=" N VAL T 12 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE T 60 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU T 7 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU T 58 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE T 9 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE T 56 " --> pdb=" O ILE T 9 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL T 96 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER T 117 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.653A 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 2252 hydrogen bonds defined for protein. 6324 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: 22.13 Time building geometry restraints manager: 17.71 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: 11824 1.46 - 1.58: 24880 1.58 - 1.70: 0 1.70 - 1.82: 496 Bond restraints: 55352 Sorted by residual: 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 3.08e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+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 2.93e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+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 2.93e+00 ... (remaining 55347 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 1633 107.04 - 113.77: 30785 113.77 - 120.50: 21565 120.50 - 127.23: 20243 127.23 - 133.96: 560 Bond angle restraints: 74786 Sorted by residual: angle pdb=" C ASN B 227 " pdb=" CA ASN B 227 " pdb=" CB ASN B 227 " ideal model delta sigma weight residual 110.42 114.55 -4.13 1.99e+00 2.53e-01 4.31e+00 angle pdb=" C ASN N 227 " pdb=" CA ASN N 227 " pdb=" CB ASN N 227 " ideal model delta sigma weight residual 110.42 114.55 -4.13 1.99e+00 2.53e-01 4.30e+00 angle pdb=" CA LYS F 50 " pdb=" CB LYS F 50 " pdb=" CG LYS F 50 " ideal model delta sigma weight residual 114.10 117.63 -3.53 2.00e+00 2.50e-01 3.11e+00 angle pdb=" CA LYS R 50 " pdb=" CB LYS R 50 " pdb=" CG LYS R 50 " ideal model delta sigma weight residual 114.10 117.57 -3.47 2.00e+00 2.50e-01 3.01e+00 angle pdb=" CA GLY M1483 " pdb=" C GLY M1483 " pdb=" N MET M1484 " ideal model delta sigma weight residual 115.34 116.74 -1.40 8.10e-01 1.52e+00 2.97e+00 ... (remaining 74781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 30793 17.90 - 35.79: 2505 35.79 - 53.69: 450 53.69 - 71.59: 98 71.59 - 89.49: 74 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 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+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 -134.79 -45.21 0 5.00e+00 4.00e-02 8.18e+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 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 33917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5836 0.030 - 0.060: 1511 0.060 - 0.090: 442 0.090 - 0.120: 523 0.120 - 0.150: 50 Chirality restraints: 8362 Sorted by residual: chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 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 5.64e-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 5.48e-01 ... (remaining 8359 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 395 " -0.039 5.00e-02 4.00e+02 5.82e-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 THR A 395 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 396 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN S 122 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" CG ASN S 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN S 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN S 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 426 2.55 - 3.14: 44606 3.14 - 3.73: 86096 3.73 - 4.31: 120717 4.31 - 4.90: 201585 Nonbonded interactions: 453430 Sorted by model distance: nonbonded pdb=" OG SER M 867 " pdb=" OG1 THR M1415 " model vdw 1.969 2.440 nonbonded pdb=" OG SER A 867 " pdb=" OG1 THR A1415 " model vdw 1.969 2.440 nonbonded pdb=" OD1 ASN M 372 " pdb=" OH TYR N 788 " model vdw 1.985 2.440 nonbonded pdb=" OD1 ASN A 372 " pdb=" OH TYR B 788 " model vdw 1.987 2.440 nonbonded pdb=" OH TYR M 763 " pdb=" OD2 ASP T 23 " model vdw 2.012 2.440 ... (remaining 453425 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 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.730 Check model and map are aligned: 0.690 Set scattering table: 0.380 Process input model: 118.750 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 0.033 55352 Z= 0.112 Angle : 0.386 5.112 74786 Z= 0.211 Chirality : 0.039 0.150 8362 Planarity : 0.002 0.058 9702 Dihedral : 14.045 89.486 21124 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 6690 helix: 2.04 (0.12), residues: 2172 sheet: 0.21 (0.16), residues: 992 loop : 0.33 (0.11), residues: 3526 *********************** 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 1823 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1823 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1823 average time/residue: 0.6260 time to fit residues: 1863.4821 Evaluate side-chains 852 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 852 time to evaluate : 4.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6934 ------------------------------------------------------------------------------- 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: 2.9990 chunk 503 optimal weight: 0.1980 chunk 279 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 520 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 387 optimal weight: 9.9990 chunk 602 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 111 ASN B 525 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 55 GLN D 66 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN G 91 GLN G 93 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 40 HIS ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1082 HIS M1410 HIS ** N 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN O 265 HIS P 66 ASN Q 65 ASN S 91 GLN S 93 ASN ** S 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 55352 Z= 0.242 Angle : 0.636 10.664 74786 Z= 0.330 Chirality : 0.046 0.310 8362 Planarity : 0.005 0.071 9702 Dihedral : 3.561 44.558 7396 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.14 % Allowed : 11.80 % Favored : 85.06 % 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: 0.67 (0.10), residues: 6690 helix: 1.23 (0.11), residues: 2316 sheet: 0.11 (0.16), residues: 1002 loop : 0.11 (0.11), residues: 3372 *********************** 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 1129 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 940 time to evaluate : 5.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 115 residues processed: 1067 average time/residue: 0.5468 time to fit residues: 987.2244 Evaluate side-chains 816 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 701 time to evaluate : 4.891 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 0 residues processed: 115 average time/residue: 0.4202 time to fit residues: 95.6599 ------------------------------------------------------------------------------- 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: 5.9990 chunk 187 optimal weight: 0.3980 chunk 501 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 604 optimal weight: 8.9990 chunk 652 optimal weight: 9.9990 chunk 537 optimal weight: 9.9990 chunk 599 optimal weight: 0.4980 chunk 205 optimal weight: 0.0370 chunk 484 optimal weight: 7.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN B 43 GLN B 344 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN E 138 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 HIS N 197 GLN N 344 GLN ** N 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 906 GLN N 941 GLN U 56 ASN U 91 HIS U 100 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55352 Z= 0.181 Angle : 0.582 9.659 74786 Z= 0.295 Chirality : 0.044 0.284 8362 Planarity : 0.004 0.074 9702 Dihedral : 3.659 41.897 7396 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 15.45 % Favored : 82.97 % 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: 0.54 (0.10), residues: 6690 helix: 1.15 (0.11), residues: 2334 sheet: 0.12 (0.16), residues: 968 loop : -0.03 (0.11), residues: 3388 *********************** 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 917 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 822 time to evaluate : 4.938 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 outliers start: 95 outliers final: 30 residues processed: 887 average time/residue: 0.5250 time to fit residues: 787.5778 Evaluate side-chains 708 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 678 time to evaluate : 5.049 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3980 time to fit residues: 29.4644 ------------------------------------------------------------------------------- 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: 10.0000 chunk 454 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 606 optimal weight: 10.0000 chunk 641 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 574 optimal weight: 20.0000 chunk 172 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN B 639 HIS ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B 906 GLN B 930 GLN B 941 GLN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN M 504 HIS ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 765 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1172 ASN ** M1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 552 ASN N 639 HIS N 731 GLN ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 825 GLN ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 986 GLN O 265 HIS ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** U 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 GLN U 91 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 55352 Z= 0.519 Angle : 0.826 11.711 74786 Z= 0.423 Chirality : 0.051 0.260 8362 Planarity : 0.006 0.077 9702 Dihedral : 4.761 41.514 7396 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.92 % Allowed : 17.21 % Favored : 78.87 % 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: -0.07 (0.10), residues: 6690 helix: 0.48 (0.11), residues: 2314 sheet: -0.31 (0.16), residues: 978 loop : -0.22 (0.11), residues: 3398 *********************** 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 969 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 733 time to evaluate : 4.962 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: 236 outliers final: 133 residues processed: 896 average time/residue: 0.5171 time to fit residues: 790.4452 Evaluate side-chains 735 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 602 time to evaluate : 4.930 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 0.4026 time to fit residues: 107.7058 ------------------------------------------------------------------------------- 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: 0.7980 chunk 364 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 477 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 547 optimal weight: 6.9990 chunk 443 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 576 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS E 132 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 23 HIS M 780 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1077 ASN M1182 GLN ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 144 HIS ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 930 GLN ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN O 265 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS V 52 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 55352 Z= 0.247 Angle : 0.619 15.222 74786 Z= 0.311 Chirality : 0.045 0.281 8362 Planarity : 0.004 0.068 9702 Dihedral : 4.319 39.798 7396 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.08 % Allowed : 19.12 % Favored : 78.80 % 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: 0.10 (0.10), residues: 6690 helix: 0.81 (0.11), residues: 2290 sheet: -0.28 (0.15), residues: 1012 loop : -0.24 (0.11), residues: 3388 *********************** 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 826 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 701 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 47 residues processed: 786 average time/residue: 0.5153 time to fit residues: 693.1345 Evaluate side-chains 667 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 620 time to evaluate : 6.207 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3903 time to fit residues: 41.7918 ------------------------------------------------------------------------------- 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: 6.9990 chunk 126 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 642 optimal weight: 1.9990 chunk 533 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS E 132 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS Q 132 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55352 Z= 0.291 Angle : 0.633 14.375 74786 Z= 0.319 Chirality : 0.046 0.326 8362 Planarity : 0.004 0.063 9702 Dihedral : 4.347 39.054 7396 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.86 % Allowed : 20.65 % Favored : 77.49 % 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: 0.12 (0.10), residues: 6690 helix: 0.88 (0.11), residues: 2308 sheet: -0.23 (0.16), residues: 990 loop : -0.30 (0.11), residues: 3392 *********************** 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 775 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 663 time to evaluate : 4.950 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: 112 outliers final: 53 residues processed: 739 average time/residue: 0.5161 time to fit residues: 651.5035 Evaluate side-chains 655 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 602 time to evaluate : 4.989 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.3890 time to fit residues: 45.8180 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 chunk 469 optimal weight: 5.9990 chunk 363 optimal weight: 2.9990 chunk 540 optimal weight: 1.9990 chunk 358 optimal weight: 0.9980 chunk 639 optimal weight: 0.9980 chunk 400 optimal weight: 0.9980 chunk 390 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 699 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1005 HIS ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 502 HIS ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55352 Z= 0.221 Angle : 0.610 15.840 74786 Z= 0.304 Chirality : 0.045 0.343 8362 Planarity : 0.004 0.063 9702 Dihedral : 4.243 36.549 7396 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 21.23 % Favored : 77.47 % 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: 0.16 (0.10), residues: 6690 helix: 0.96 (0.11), residues: 2326 sheet: -0.21 (0.16), residues: 984 loop : -0.32 (0.11), residues: 3380 *********************** 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 743 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 665 time to evaluate : 4.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 78 outliers final: 34 residues processed: 709 average time/residue: 0.5208 time to fit residues: 630.7644 Evaluate side-chains 654 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 620 time to evaluate : 4.978 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4395 time to fit residues: 33.7677 ------------------------------------------------------------------------------- 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: 10.0000 chunk 255 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 192 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 406 optimal weight: 3.9990 chunk 436 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 503 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 ASN M 809 HIS ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55352 Z= 0.224 Angle : 0.624 16.277 74786 Z= 0.309 Chirality : 0.045 0.331 8362 Planarity : 0.004 0.063 9702 Dihedral : 4.239 35.748 7396 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.90 % Allowed : 21.96 % Favored : 77.14 % 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: 0.20 (0.10), residues: 6690 helix: 1.02 (0.11), residues: 2332 sheet: -0.19 (0.16), residues: 976 loop : -0.32 (0.11), residues: 3382 *********************** 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 702 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 648 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 15 residues processed: 684 average time/residue: 0.5157 time to fit residues: 608.1882 Evaluate side-chains 622 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 607 time to evaluate : 4.958 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3856 time to fit residues: 17.8209 ------------------------------------------------------------------------------- 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: 7.9990 chunk 613 optimal weight: 0.0060 chunk 559 optimal weight: 0.7980 chunk 596 optimal weight: 0.8980 chunk 612 optimal weight: 6.9990 chunk 358 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 468 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 538 optimal weight: 0.0270 chunk 564 optimal weight: 1.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 HIS ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 777 ASN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS G 93 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 500 GLN N 777 ASN N 825 GLN ** N 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55352 Z= 0.180 Angle : 0.615 16.316 74786 Z= 0.303 Chirality : 0.045 0.340 8362 Planarity : 0.004 0.064 9702 Dihedral : 4.147 35.060 7396 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.56 % Allowed : 22.78 % Favored : 76.66 % 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: 0.25 (0.10), residues: 6690 helix: 1.05 (0.11), residues: 2340 sheet: -0.16 (0.16), residues: 938 loop : -0.28 (0.11), residues: 3412 *********************** 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 687 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 653 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 676 average time/residue: 0.5250 time to fit residues: 609.0648 Evaluate side-chains 620 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 609 time to evaluate : 5.025 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3976 time to fit residues: 15.1116 ------------------------------------------------------------------------------- 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: 10.0000 chunk 391 optimal weight: 0.9980 chunk 630 optimal weight: 9.9990 chunk 384 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 438 optimal weight: 0.0170 chunk 661 optimal weight: 8.9990 chunk 608 optimal weight: 4.9990 chunk 526 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS ** N 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 55352 Z= 0.251 Angle : 0.647 15.600 74786 Z= 0.319 Chirality : 0.045 0.331 8362 Planarity : 0.004 0.104 9702 Dihedral : 4.230 35.131 7396 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 23.21 % Favored : 76.48 % 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: 0.21 (0.10), residues: 6690 helix: 1.00 (0.11), residues: 2350 sheet: -0.18 (0.16), residues: 944 loop : -0.29 (0.11), residues: 3396 ********************** 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 637 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 618 time to evaluate : 5.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 632 average time/residue: 0.5164 time to fit residues: 562.8396 Evaluate side-chains 596 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 588 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3837 time to fit residues: 12.6167 ------------------------------------------------------------------------------- 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: 0.0270 chunk 418 optimal weight: 7.9990 chunk 561 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 527 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 541 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.115804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092515 restraints weight = 132159.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092312 restraints weight = 121013.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093063 restraints weight = 91325.548| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55352 Z= 0.238 Angle : 0.646 16.331 74786 Z= 0.319 Chirality : 0.045 0.359 8362 Planarity : 0.004 0.085 9702 Dihedral : 4.260 34.290 7396 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.38 % Allowed : 23.27 % Favored : 76.34 % 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: 0.23 (0.10), residues: 6690 helix: 0.99 (0.11), residues: 2360 sheet: -0.12 (0.16), residues: 916 loop : -0.28 (0.11), residues: 3414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12495.20 seconds wall clock time: 221 minutes 36.15 seconds (13296.15 seconds total)