Starting phenix.real_space_refine on Tue Apr 16 13:08:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buu_16246/04_2024/8buu_16246_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 16 8.98 5 Zn 4 6.06 5 P 4588 5.49 5 Mg 85 5.21 5 S 144 5.16 5 C 72859 2.51 5 N 26866 2.21 5 O 40203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 144765 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 61256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2852, 61256 Inner-chain residues flagged as termini: ['pdbres=" G A1220 "'] Classifications: {'RNA': 2852} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 290, 'rna2p_pyr': 139, 'rna3p': 1, 'rna3p_pur': 1367, 'rna3p_pyr': 1053} Link IDs: {'rna2p': 430, 'rna3p': 2421} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 52, 'rna3p_pyr': 44} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2094 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "E" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1567 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "F" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1405 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'TRANS': 117} Chain: "R" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 795 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "T" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 733 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "U" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "V" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain: "W" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 610 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 468 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "Y" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1818 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "u" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 199 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain breaks: 1 Chain: "0" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "2" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'TRANS': 64} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "p" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 81} Chain: "r" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "t" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 658 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "d" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1604 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain: "e" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1208 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "h" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "a" Number of atoms: 32991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1538, 32991 Classifications: {'RNA': 1538} Modifications used: {'rna2p_pur': 117, 'rna2p_pyr': 86, 'rna3p_pur': 754, 'rna3p_pyr': 581} Link IDs: {'rna2p': 203, 'rna3p': 1334} Chain breaks: 1 Chain: "k" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 847 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "l" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1047 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "o" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 730 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "q" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 676 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1611 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain: "g" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1246 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 994 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "j" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 788 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "m" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 498 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "s" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "9" Number of atoms: 4684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4684 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 11, 'TRANS': 561} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Unusual residues: {' K': 14, ' MG': 82} Classifications: {'undetermined': 96} Link IDs: {None: 95} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 88655 SG CYS 0 30 138.643 247.707 126.541 1.00 40.14 S ATOM 88674 SG CYS 0 33 136.185 249.706 124.265 1.00 32.63 S ATOM 88752 SG CYS 0 43 137.247 246.332 123.247 1.00 43.35 S ATOM 88772 SG CYS 0 46 139.579 249.279 123.037 1.00 36.26 S ATOM 88891 SG CYS 1 9 42.647 134.592 95.127 1.00 25.66 S ATOM 88913 SG CYS 1 12 42.128 137.678 93.520 1.00 24.00 S ATOM 89122 SG CYS 1 36 41.804 137.967 96.881 1.00 20.40 S ATOM 90209 SG CYS 4 11 124.625 145.998 175.128 1.00 40.48 S ATOM 90233 SG CYS 4 14 123.240 149.240 173.606 1.00 42.20 S ATOM 90337 SG CYS 4 27 126.554 149.240 175.520 1.00 38.82 S ATOM A0U1O SG CYS n 24 141.901 55.838 113.095 1.00 37.02 S ATOM A0U2E SG CYS n 27 143.013 59.491 113.737 1.00 25.35 S ATOM A0U5D SG CYS n 40 141.336 58.784 110.556 1.00 24.39 S ATOM A0U62 SG CYS n 43 144.719 57.336 111.096 1.00 47.34 S Time building chain proxies: 56.31, per 1000 atoms: 0.39 Number of scatterers: 144765 At special positions: 0 Unit cell: (268.96, 276.34, 223.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 16 19.00 S 144 16.00 P 4588 15.00 Mg 85 11.99 O 40203 8.00 N 26866 7.00 C 72859 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: 62.71 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 05001 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 33 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 43 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 46 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 30 " pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 12 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 36 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 9 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN n5001 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 43 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 27 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 40 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 24 " Number of angles added : 15 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10760 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 184 helices and 78 sheets defined 40.0% alpha, 19.5% beta 1508 base pairs and 2506 stacking pairs defined. Time for finding SS restraints: 82.26 Creating SS restraints... Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.587A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.633A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.945A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.462A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.229A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.011A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.319A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 4.045A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLU D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 121 through 127 removed outlier: 4.103A pdb=" N HIS D 126 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.574A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 6.297A pdb=" N ARG E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 Processing helix chain 'E' and resid 135 through 147 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 190 removed outlier: 5.062A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 207 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 40 through 46 removed outlier: 5.044A pdb=" N VAL F 44 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.634A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.629A pdb=" N VAL F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.977A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.506A pdb=" N LYS G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 Processing helix chain 'G' and resid 138 through 154 removed outlier: 4.131A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.652A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 97 through 111 removed outlier: 3.526A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 113 through 124 removed outlier: 4.040A pdb=" N LYS J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN J 124 " --> pdb=" O PHE J 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.144A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.702A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.505A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.898A pdb=" N GLY L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.886A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.246A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.765A pdb=" N TYR N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.591A pdb=" N ILE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 22 removed outlier: 4.121A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.637A pdb=" N GLU P 6 " --> pdb=" O GLN P 2 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLN P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.494A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 3.568A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 4.422A pdb=" N HIS Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 40 through 54 removed outlier: 4.281A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 73 removed outlier: 3.568A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 119 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.888A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Proline residue: S 45 - end of helix Processing helix chain 'T' and resid 3 through 9 removed outlier: 4.002A pdb=" N VAL T 7 " --> pdb=" O ASP T 3 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU T 8 " --> pdb=" O PRO T 4 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 9' Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.772A pdb=" N THR T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.378A pdb=" N VAL U 68 " --> pdb=" O HIS U 64 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N MET U 69 " --> pdb=" O VAL U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 69' Processing helix chain 'X' and resid 50 through 57 removed outlier: 4.042A pdb=" N SER X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.588A pdb=" N ASP Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 Processing helix chain 'Y' and resid 39 through 66 removed outlier: 4.606A pdb=" N ILE Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.729A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 32 removed outlier: 3.754A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.546A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 5.052A pdb=" N ASP b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 Processing helix chain 'b' and resid 125 through 130 Proline residue: b 130 - end of helix Processing helix chain 'b' and resid 131 through 148 removed outlier: 3.607A pdb=" N PHE b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.854A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 226 Processing helix chain '0' and resid 9 through 21 removed outlier: 5.121A pdb=" N HIS 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.097A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.578A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 3.986A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 47 removed outlier: 3.909A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER 3 47 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 59 removed outlier: 3.598A pdb=" N ARG 3 57 " --> pdb=" O GLY 3 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.778A pdb=" N GLY f 34 " --> pdb=" O LEU f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 5.703A pdb=" N ASP f 83 " --> pdb=" O ALA f 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 88 Processing helix chain 'r' and resid 16 through 22 Processing helix chain 'r' and resid 30 through 39 removed outlier: 4.006A pdb=" N LYS r 36 " --> pdb=" O ASP r 32 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 71 Processing helix chain 't' and resid 4 through 42 Processing helix chain 't' and resid 43 through 65 Processing helix chain 't' and resid 68 through 87 removed outlier: 3.974A pdb=" N LEU t 86 " --> pdb=" O LYS t 82 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.737A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 28 removed outlier: 6.913A pdb=" N GLU d 27 " --> pdb=" O GLY d 23 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS d 28 " --> pdb=" O LYS d 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 23 through 28' Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 79 removed outlier: 3.763A pdb=" N LYS d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 Processing helix chain 'd' and resid 94 through 102 Processing helix chain 'd' and resid 106 through 117 Processing helix chain 'd' and resid 148 through 158 Processing helix chain 'd' and resid 181 through 186 removed outlier: 6.672A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.773A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 10 removed outlier: 3.916A pdb=" N LEU e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU e 10 " --> pdb=" O PRO e 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 5 through 10' Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.577A pdb=" N ASN e 70 " --> pdb=" O ASP e 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.609A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 166 Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'k' and resid 48 through 53 removed outlier: 3.513A pdb=" N GLY k 53 " --> pdb=" O ALA k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 removed outlier: 4.062A pdb=" N SER k 60 " --> pdb=" O GLY k 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix No H-bonds generated for 'chain 'k' and resid 56 through 62' Processing helix chain 'k' and resid 63 through 80 removed outlier: 3.825A pdb=" N GLU k 78 " --> pdb=" O LYS k 74 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS k 79 " --> pdb=" O GLY k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 94 through 106 removed outlier: 3.626A pdb=" N GLY k 106 " --> pdb=" O LEU k 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 26 removed outlier: 3.806A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 126 through 131 removed outlier: 3.840A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.822A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.576A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.608A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.668A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.571A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.667A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 5.762A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 153 removed outlier: 5.184A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.526A pdb=" N GLU i 89 " --> pdb=" O ARG i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 102 removed outlier: 4.849A pdb=" N THR i 96 " --> pdb=" O PRO i 92 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR i 97 " --> pdb=" O GLU i 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.595A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.813A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.544A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR m 49 " --> pdb=" O VAL m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.839A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS m 64 " --> pdb=" O ILE m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 13 removed outlier: 5.174A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.506A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.604A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.151A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain '9' and resid 46 through 56 Processing helix chain '9' and resid 79 through 88 removed outlier: 3.864A pdb=" N GLU 9 83 " --> pdb=" O SER 9 79 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN 9 88 " --> pdb=" O VAL 9 84 " (cutoff:3.500A) Processing helix chain '9' and resid 89 through 94 removed outlier: 3.644A pdb=" N GLU 9 93 " --> pdb=" O GLN 9 89 " (cutoff:3.500A) Processing helix chain '9' and resid 95 through 107 removed outlier: 3.581A pdb=" N LEU 9 99 " --> pdb=" O GLU 9 95 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER 9 105 " --> pdb=" O GLN 9 101 " (cutoff:3.500A) Processing helix chain '9' and resid 115 through 122 Processing helix chain '9' and resid 123 through 139 removed outlier: 3.989A pdb=" N LYS 9 139 " --> pdb=" O VAL 9 135 " (cutoff:3.500A) Processing helix chain '9' and resid 153 through 167 removed outlier: 3.503A pdb=" N LYS 9 166 " --> pdb=" O SER 9 162 " (cutoff:3.500A) Processing helix chain '9' and resid 177 through 185 Processing helix chain '9' and resid 203 through 250 removed outlier: 4.609A pdb=" N THR 9 250 " --> pdb=" O HIS 9 246 " (cutoff:3.500A) Processing helix chain '9' and resid 254 through 261 removed outlier: 6.023A pdb=" N ILE 9 261 " --> pdb=" O GLU 9 257 " (cutoff:3.500A) Processing helix chain '9' and resid 262 through 292 Processing helix chain '9' and resid 355 through 365 Processing helix chain '9' and resid 397 through 403 Processing helix chain '9' and resid 406 through 421 Processing helix chain '9' and resid 423 through 430 removed outlier: 3.651A pdb=" N LYS 9 429 " --> pdb=" O GLN 9 425 " (cutoff:3.500A) Proline residue: 9 430 - end of helix Processing helix chain '9' and resid 435 through 451 removed outlier: 4.519A pdb=" N LYS 9 450 " --> pdb=" O ASP 9 446 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU 9 451 " --> pdb=" O MET 9 447 " (cutoff:3.500A) Processing helix chain '9' and resid 465 through 479 removed outlier: 3.521A pdb=" N GLU 9 478 " --> pdb=" O GLN 9 474 " (cutoff:3.500A) Processing helix chain '9' and resid 489 through 497 Processing helix chain '9' and resid 514 through 521 removed outlier: 3.734A pdb=" N LYS 9 521 " --> pdb=" O GLU 9 517 " (cutoff:3.500A) Processing helix chain '9' and resid 527 through 551 removed outlier: 3.887A pdb=" N GLU 9 531 " --> pdb=" O ASP 9 527 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA 9 532 " --> pdb=" O ARG 9 528 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU 9 549 " --> pdb=" O GLY 9 545 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE 9 550 " --> pdb=" O GLU 9 546 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP 9 551 " --> pdb=" O LEU 9 547 " (cutoff:3.500A) Processing helix chain '9' and resid 554 through 575 removed outlier: 4.130A pdb=" N TYR 9 558 " --> pdb=" O ASN 9 554 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG 9 559 " --> pdb=" O PRO 9 555 " (cutoff:3.500A) Processing helix chain '9' and resid 388 through 393 removed outlier: 3.635A pdb=" N LEU 9 392 " --> pdb=" O VAL 9 389 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER 9 393 " --> pdb=" O ALA 9 390 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.621A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N MET C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.694A pdb=" N THR C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY C 127 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N MET C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 5.441A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.071A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 3 through 7 removed outlier: 5.639A pdb=" N LYS D 3 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.605A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.830A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN D 95 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 105 through 109 removed outlier: 4.186A pdb=" N GLU D 106 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.268A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 12, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.794A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.059A pdb=" N LYS F 72 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU F 81 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.932A pdb=" N ASN G 20 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN G 23 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG G 36 " --> pdb=" O VAL G 25 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 43 through 46 Processing sheet with id= 16, first strand: chain 'G' and resid 83 through 90 removed outlier: 3.856A pdb=" N LEU G 90 " --> pdb=" O THR G 130 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N THR G 130 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= 18, first strand: chain 'J' and resid 53 through 58 removed outlier: 5.040A pdb=" N ASP J 20 " --> pdb=" O TYR J 141 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 75 through 79 removed outlier: 7.230A pdb=" N GLY J 84 " --> pdb=" O THR J 79 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 17 through 21 removed outlier: 6.276A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR K 6 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 22, first strand: chain 'K' and resid 68 through 72 removed outlier: 6.709A pdb=" N ALA K 69 " --> pdb=" O TYR K 76 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR K 76 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG K 71 " --> pdb=" O GLY K 74 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 24, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.781A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU M 31 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 72 through 75 removed outlier: 6.487A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 29 through 33 Processing sheet with id= 27, first strand: chain 'O' and resid 54 through 57 removed outlier: 3.556A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.562A pdb=" N THR P 25 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS P 83 " --> pdb=" O HIS P 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.727A pdb=" N LYS P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.898A pdb=" N TYR R 2 " --> pdb=" O GLY R 42 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.106A pdb=" N GLN R 18 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR R 59 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU R 31 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= 33, first strand: chain 'R' and resid 64 through 67 Processing sheet with id= 34, first strand: chain 'R' and resid 70 through 77 removed outlier: 4.186A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 2 through 8 removed outlier: 6.782A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 73 through 79 removed outlier: 4.695A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 81 through 88 removed outlier: 4.039A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 25 through 30 removed outlier: 4.332A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS T 62 " --> pdb=" O THR T 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG T 75 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS T 60 " --> pdb=" O ARG T 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG T 77 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN T 58 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA T 79 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE T 56 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL T 81 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL T 54 " --> pdb=" O VAL T 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.615A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 39 through 44 removed outlier: 5.155A pdb=" N ASN U 39 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 81 through 85 Processing sheet with id= 42, first strand: chain 'W' and resid 45 through 48 removed outlier: 4.785A pdb=" N GLN W 48 " --> pdb=" O ASP W 65 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP W 65 " --> pdb=" O GLN W 48 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 74 through 79 Processing sheet with id= 44, first strand: chain 'X' and resid 11 through 19 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'X' and resid 35 through 38 Processing sheet with id= 46, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.348A pdb=" N GLN Z 33 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS Z 3 " --> pdb=" O GLN Z 59 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU Z 53 " --> pdb=" O LYS Z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 90 through 93 removed outlier: 3.891A pdb=" N TYR b 90 " --> pdb=" O ILE b 67 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '1' and resid 3 through 8 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain '1' and resid 30 through 34 removed outlier: 5.653A pdb=" N VAL 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 51, first strand: chain 'f' and resid 39 through 43 removed outlier: 3.507A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LYS f 3 " --> pdb=" O GLU f 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 44 through 48 removed outlier: 6.534A pdb=" N ARG f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 5 through 12 Processing sheet with id= 54, first strand: chain 'd' and resid 136 through 140 removed outlier: 4.474A pdb=" N GLN d 137 " --> pdb=" O PHE d 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TYR d 164 " --> pdb=" O THR d 177 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 11 through 16 Processing sheet with id= 56, first strand: chain 'e' and resid 83 through 88 removed outlier: 7.665A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN e 93 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA e 99 " --> pdb=" O ASP e 122 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 32 through 41 removed outlier: 6.573A pdb=" N HIS e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.310A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.501A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 44 through 47 removed outlier: 3.922A pdb=" N THR k 83 " --> pdb=" O GLU k 19 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL k 86 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 27 through 30 Processing sheet with id= 62, first strand: chain 'l' and resid 42 through 45 removed outlier: 5.132A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 49 through 54 removed outlier: 5.304A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.846A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 21 through 32 removed outlier: 4.334A pdb=" N LYS q 21 " --> pdb=" O ASP q 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.596A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'c' and resid 163 through 169 Processing sheet with id= 68, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.209A pdb=" N VAL g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'i' and resid 5 through 11 removed outlier: 6.274A pdb=" N TYR i 61 " --> pdb=" O GLU i 25 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG i 27 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.598A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 72, first strand: chain 's' and resid 30 through 34 removed outlier: 4.552A pdb=" N HIS s 47 " --> pdb=" O ILE s 62 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '9' and resid 28 through 32 Processing sheet with id= 74, first strand: chain '9' and resid 36 through 41 Processing sheet with id= 75, first strand: chain '9' and resid 72 through 76 removed outlier: 5.708A pdb=" N ASP 9 146 " --> pdb=" O LEU 9 76 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '9' and resid 337 through 341 removed outlier: 7.484A pdb=" N ILE 9 317 " --> pdb=" O SER 9 377 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '9' and resid 345 through 350 Processing sheet with id= 78, first strand: chain '9' and resid 381 through 386 removed outlier: 3.595A pdb=" N THR 9 482 " --> pdb=" O ASP 9 453 " (cutoff:3.500A) 2070 hydrogen bonds defined for protein. 6102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3768 hydrogen bonds 6016 hydrogen bond angles 0 basepair planarities 1508 basepair parallelities 2506 stacking parallelities Total time for adding SS restraints: 235.43 Time building geometry restraints manager: 68.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20046 1.33 - 1.45: 65011 1.45 - 1.57: 62608 1.57 - 1.69: 9165 1.69 - 1.81: 264 Bond restraints: 157094 Sorted by residual: bond pdb=" C3' ATP 9 701 " pdb=" C4' ATP 9 701 " ideal model delta sigma weight residual 1.305 1.521 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C3' ATP 9 702 " pdb=" C4' ATP 9 702 " ideal model delta sigma weight residual 1.305 1.520 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C4' ATP 9 702 " pdb=" O4' ATP 9 702 " ideal model delta sigma weight residual 1.608 1.441 0.167 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C4' ATP 9 701 " pdb=" O4' ATP 9 701 " ideal model delta sigma weight residual 1.608 1.442 0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C2 OMG A2280 " pdb=" N3 OMG A2280 " ideal model delta sigma weight residual 1.466 1.303 0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 157089 not shown) Histogram of bond angle deviations from ideal: 98.29 - 106.59: 28143 106.59 - 114.89: 102436 114.89 - 123.19: 79912 123.19 - 131.49: 23076 131.49 - 139.79: 1202 Bond angle restraints: 234769 Sorted by residual: angle pdb=" C1' ATP 9 701 " pdb=" N9 ATP 9 701 " pdb=" C8 ATP 9 701 " ideal model delta sigma weight residual 92.72 127.43 -34.71 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C1' ATP 9 702 " pdb=" N9 ATP 9 702 " pdb=" C8 ATP 9 702 " ideal model delta sigma weight residual 92.72 127.15 -34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C1' ATP 9 701 " pdb=" N9 ATP 9 701 " pdb=" C4 ATP 9 701 " ideal model delta sigma weight residual 147.86 126.89 20.97 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C1' ATP 9 702 " pdb=" N9 ATP 9 702 " pdb=" C4 ATP 9 702 " ideal model delta sigma weight residual 147.86 127.19 20.67 3.00e+00 1.11e-01 4.75e+01 angle pdb=" C1' OMG A2280 " pdb=" N9 OMG A2280 " pdb=" C4 OMG A2280 " ideal model delta sigma weight residual 108.29 126.82 -18.53 3.00e+00 1.11e-01 3.81e+01 ... (remaining 234764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 89323 35.92 - 71.84: 10076 71.84 - 107.77: 1242 107.77 - 143.69: 35 143.69 - 179.61: 38 Dihedral angle restraints: 100714 sinusoidal: 83998 harmonic: 16716 Sorted by residual: dihedral pdb=" C4' U A1535 " pdb=" C3' U A1535 " pdb=" C2' U A1535 " pdb=" C1' U A1535 " ideal model delta sinusoidal sigma weight residual -35.00 30.68 -65.68 1 8.00e+00 1.56e-02 8.82e+01 dihedral pdb=" O4' C A2695 " pdb=" C1' C A2695 " pdb=" N1 C A2695 " pdb=" C2 C A2695 " ideal model delta sinusoidal sigma weight residual 200.00 20.39 179.61 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 476 " pdb=" C1' U a 476 " pdb=" N1 U a 476 " pdb=" C2 U a 476 " ideal model delta sinusoidal sigma weight residual -160.00 10.01 -170.01 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 100711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 28642 0.071 - 0.142: 1254 0.142 - 0.213: 28 0.213 - 0.285: 2 0.285 - 0.356: 2 Chirality restraints: 29928 Sorted by residual: chirality pdb=" C3' A A2468 " pdb=" C4' A A2468 " pdb=" O3' A A2468 " pdb=" C2' A A2468 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C3' A A2805 " pdb=" C4' A A2805 " pdb=" O3' A A2805 " pdb=" C2' A A2805 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' A A1339 " pdb=" C4' A A1339 " pdb=" O3' A A1339 " pdb=" C2' A A1339 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 29925 not shown) Planarity restraints: 12676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP 9 701 " -0.449 2.00e-02 2.50e+03 6.19e-01 8.61e+03 pdb=" C2' ATP 9 701 " 0.714 2.00e-02 2.50e+03 pdb=" C3' ATP 9 701 " 0.306 2.00e-02 2.50e+03 pdb=" C4' ATP 9 701 " -0.225 2.00e-02 2.50e+03 pdb=" C5' ATP 9 701 " 0.891 2.00e-02 2.50e+03 pdb=" N9 ATP 9 701 " -0.003 2.00e-02 2.50e+03 pdb=" O2' ATP 9 701 " 0.513 2.00e-02 2.50e+03 pdb=" O3' ATP 9 701 " -0.827 2.00e-02 2.50e+03 pdb=" O4' ATP 9 701 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP 9 702 " 0.454 2.00e-02 2.50e+03 6.14e-01 8.48e+03 pdb=" C2' ATP 9 702 " -0.710 2.00e-02 2.50e+03 pdb=" C3' ATP 9 702 " -0.326 2.00e-02 2.50e+03 pdb=" C4' ATP 9 702 " 0.218 2.00e-02 2.50e+03 pdb=" C5' ATP 9 702 " -0.877 2.00e-02 2.50e+03 pdb=" N9 ATP 9 702 " -0.007 2.00e-02 2.50e+03 pdb=" O2' ATP 9 702 " -0.489 2.00e-02 2.50e+03 pdb=" O3' ATP 9 702 " 0.799 2.00e-02 2.50e+03 pdb=" O4' ATP 9 702 " 0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2280 " 0.019 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' OMG A2280 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMG A2280 " 0.704 2.00e-02 2.50e+03 pdb=" C3' OMG A2280 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG A2280 " -0.547 2.00e-02 2.50e+03 pdb=" C2' OMG A2280 " -0.231 2.00e-02 2.50e+03 pdb=" O2' OMG A2280 " 0.874 2.00e-02 2.50e+03 pdb=" C1' OMG A2280 " 0.213 2.00e-02 2.50e+03 pdb=" N9 OMG A2280 " -0.880 2.00e-02 2.50e+03 ... (remaining 12673 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.43: 681 2.43 - 3.11: 103370 3.11 - 3.79: 330433 3.79 - 4.46: 515544 4.46 - 5.14: 667995 Nonbonded interactions: 1618023 Sorted by model distance: nonbonded pdb=" O3G ATP 9 701 " pdb="MG MG 9 703 " model vdw 1.758 2.170 nonbonded pdb=" OP1 A A1659 " pdb="MG MG A3047 " model vdw 1.765 2.170 nonbonded pdb=" OP1 A A1809 " pdb="MG MG A3071 " model vdw 1.818 2.170 nonbonded pdb=" OP2 G A 909 " pdb="MG MG A3043 " model vdw 1.835 2.170 nonbonded pdb=" O6 G A 614 " pdb="MG MG A3006 " model vdw 1.848 2.170 ... (remaining 1618018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 18.330 Check model and map are aligned: 1.640 Set scattering table: 1.020 Process input model: 570.470 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 609.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.004 0.216 157094 Z= 0.272 Angle : 0.558 34.709 234769 Z= 0.305 Chirality : 0.034 0.356 29928 Planarity : 0.012 0.619 12676 Dihedral : 22.720 179.611 89954 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 0.95 % Allowed : 5.70 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 5767 helix: -0.33 (0.10), residues: 2008 sheet: -0.79 (0.14), residues: 1121 loop : -0.76 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 18 HIS 0.008 0.001 HIS C 230 PHE 0.014 0.002 PHE d 68 TYR 0.029 0.002 TYR X 48 ARG 0.061 0.002 ARG 9 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1824 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1777 time to evaluate : 6.566 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: R 31 GLU cc_start: 0.6384 (mp0) cc_final: 0.5313 (mp0) REVERT: T 19 ASP cc_start: 0.6469 (t0) cc_final: 0.6209 (t0) REVERT: b 91 TYR cc_start: 0.6084 (p90) cc_final: 0.5448 (p90) REVERT: q 52 ASN cc_start: 0.7314 (m110) cc_final: 0.6820 (m-40) REVERT: q 66 THR cc_start: 0.7889 (p) cc_final: 0.7152 (p) REVERT: j 28 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7267 (t) outliers start: 47 outliers final: 7 residues processed: 1796 average time/residue: 1.9292 time to fit residues: 5130.2858 Evaluate side-chains 1432 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1424 time to evaluate : 6.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 52 ASP Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain j residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 20.0000 chunk 773 optimal weight: 40.0000 chunk 428 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 521 optimal weight: 8.9990 chunk 413 optimal weight: 9.9990 chunk 799 optimal weight: 20.0000 chunk 309 optimal weight: 0.0010 chunk 486 optimal weight: 0.9990 chunk 595 optimal weight: 0.8980 chunk 926 optimal weight: 20.0000 overall best weight: 3.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN F 63 GLN L 17 ASN L 27 ASN O 8 ASN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 28 GLN S 37 ASN X 17 ASN 3 35 ASN r 69 GLN d 50 GLN d 67 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 70 ASN k 17 ASN l 37 ASN c 3 GLN ** c 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN g 129 ASN i 126 GLN n 19 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 19 HIS 9 286 GLN 9 538 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 157094 Z= 0.186 Angle : 0.607 27.284 234769 Z= 0.311 Chirality : 0.035 0.271 29928 Planarity : 0.005 0.127 12676 Dihedral : 23.364 179.455 78041 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.14 % Rotamer: Outliers : 3.66 % Allowed : 18.26 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 5767 helix: 1.27 (0.11), residues: 2038 sheet: -0.43 (0.14), residues: 1175 loop : -0.28 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 9 136 HIS 0.007 0.001 HIS c 33 PHE 0.017 0.002 PHE g 62 TYR 0.029 0.002 TYR r 75 ARG 0.014 0.001 ARG 9 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1740 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1559 time to evaluate : 6.644 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: J 127 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7451 (ttp-170) REVERT: K 54 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8539 (tttm) REVERT: M 83 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6943 (mmm) REVERT: P 1 MET cc_start: 0.5496 (ppp) cc_final: 0.5208 (pp-130) REVERT: Q 94 MET cc_start: 0.7336 (mmt) cc_final: 0.7117 (mmt) REVERT: W 84 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7463 (mtt180) REVERT: 0 49 TYR cc_start: 0.5891 (p90) cc_final: 0.5303 (p90) REVERT: q 52 ASN cc_start: 0.7298 (m110) cc_final: 0.6892 (m-40) REVERT: j 27 GLU cc_start: 0.6368 (tp30) cc_final: 0.5815 (tp30) outliers start: 181 outliers final: 64 residues processed: 1619 average time/residue: 1.9399 time to fit residues: 4725.3542 Evaluate side-chains 1511 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1443 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 2 GLN Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 45 GLU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain k residue 17 ASN Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 20.0000 chunk 287 optimal weight: 30.0000 chunk 770 optimal weight: 20.0000 chunk 630 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 927 optimal weight: 20.0000 chunk 1002 optimal weight: 20.0000 chunk 826 optimal weight: 20.0000 chunk 920 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 744 optimal weight: 20.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN F 63 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN N 61 GLN S 28 GLN W 94 GLN Y 36 GLN ** b 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 GLN t 42 ASN d 50 GLN d 64 ASN e 70 ASN ** h 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 17 ASN l 37 ASN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN g 40 GLN g 64 GLN g 86 GLN g 129 ASN i 126 GLN s 47 HIS 9 97 HIS 9 224 GLN 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 157094 Z= 0.485 Angle : 0.657 18.146 234769 Z= 0.340 Chirality : 0.040 0.377 29928 Planarity : 0.005 0.138 12676 Dihedral : 23.290 179.649 78032 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 5.01 % Allowed : 20.40 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5767 helix: 1.51 (0.11), residues: 2029 sheet: -0.13 (0.15), residues: 1114 loop : -0.10 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP b 23 HIS 0.008 0.001 HIS c 33 PHE 0.029 0.002 PHE F 138 TYR 0.027 0.002 TYR g 44 ARG 0.018 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1687 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1439 time to evaluate : 6.002 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: K 54 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8572 (tttm) REVERT: T 46 ILE cc_start: 0.7970 (mp) cc_final: 0.7763 (mp) REVERT: U 99 GLN cc_start: 0.7462 (mp10) cc_final: 0.7088 (mp10) REVERT: W 84 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7497 (mtt180) REVERT: e 43 ASN cc_start: 0.7858 (t0) cc_final: 0.7426 (t0) REVERT: e 142 GLN cc_start: 0.7162 (tm-30) cc_final: 0.6898 (tm-30) REVERT: h 91 SER cc_start: 0.7737 (m) cc_final: 0.7518 (m) REVERT: h 110 GLN cc_start: 0.7565 (mp10) cc_final: 0.7167 (mp10) REVERT: k 79 HIS cc_start: 0.6694 (m90) cc_final: 0.6457 (m90) REVERT: j 97 ASP cc_start: 0.5664 (t0) cc_final: 0.5297 (t0) REVERT: s 53 ASP cc_start: 0.6987 (p0) cc_final: 0.6782 (p0) outliers start: 248 outliers final: 119 residues processed: 1533 average time/residue: 1.8897 time to fit residues: 4306.2951 Evaluate side-chains 1495 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1374 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 2 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 84 ARG Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 41 ASN Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 34 THR Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 58 ASP Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain 9 residue 143 LEU Chi-restraints excluded: chain 9 residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 9.9990 chunk 697 optimal weight: 50.0000 chunk 481 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 442 optimal weight: 5.9990 chunk 623 optimal weight: 7.9990 chunk 931 optimal weight: 20.0000 chunk 985 optimal weight: 9.9990 chunk 486 optimal weight: 5.9990 chunk 882 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN Q 108 GLN S 28 GLN 1 4 ASN p 88 GLN t 42 ASN d 64 ASN ** d 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN l 59 ASN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 GLN ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 133 GLN c 136 GLN g 40 GLN g 84 ASN g 129 ASN i 126 GLN m 32 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 463 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 157094 Z= 0.282 Angle : 0.588 17.435 234769 Z= 0.304 Chirality : 0.035 0.320 29928 Planarity : 0.004 0.129 12676 Dihedral : 23.355 179.537 78032 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Rotamer: Outliers : 4.02 % Allowed : 22.18 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 5767 helix: 1.66 (0.11), residues: 2032 sheet: -0.07 (0.15), residues: 1137 loop : -0.01 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 9 136 HIS 0.007 0.001 HIS c 33 PHE 0.043 0.002 PHE d 68 TYR 0.049 0.002 TYR i 94 ARG 0.012 0.001 ARG i 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1685 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1486 time to evaluate : 6.070 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: K 54 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8564 (tttm) REVERT: T 46 ILE cc_start: 0.7856 (mp) cc_final: 0.7649 (mp) REVERT: f 13 ASN cc_start: 0.5991 (p0) cc_final: 0.5781 (p0) REVERT: f 15 ASP cc_start: 0.6295 (p0) cc_final: 0.5644 (p0) REVERT: r 27 ASP cc_start: 0.6422 (t0) cc_final: 0.6020 (t0) REVERT: e 43 ASN cc_start: 0.7774 (t0) cc_final: 0.7336 (t0) REVERT: e 142 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6809 (tm-30) REVERT: h 69 ASN cc_start: 0.7818 (p0) cc_final: 0.7470 (p0) REVERT: h 99 ASN cc_start: 0.7492 (t0) cc_final: 0.7187 (t0) REVERT: h 110 GLN cc_start: 0.7547 (mp10) cc_final: 0.7127 (mp10) outliers start: 199 outliers final: 119 residues processed: 1556 average time/residue: 1.7700 time to fit residues: 4122.8789 Evaluate side-chains 1525 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1405 time to evaluate : 6.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 2 GLN Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 95 GLN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 52 ASP Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 34 THR Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain 9 residue 141 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 734 optimal weight: 30.0000 chunk 406 optimal weight: 20.0000 chunk 841 optimal weight: 20.0000 chunk 681 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 503 optimal weight: 9.9990 chunk 884 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 overall best weight: 12.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN Q 108 GLN R 18 GLN S 28 GLN Y 4 ASN 1 4 ASN r 57 GLN d 59 HIS d 64 ASN d 67 GLN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN e 70 ASN e 93 ASN l 59 ASN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 133 GLN c 136 GLN g 64 GLN g 122 ASN g 129 ASN i 32 ASN i 126 GLN n 19 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 463 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 157094 Z= 0.430 Angle : 0.638 17.372 234769 Z= 0.330 Chirality : 0.038 0.366 29928 Planarity : 0.005 0.134 12676 Dihedral : 23.299 179.578 78032 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 4.99 % Allowed : 23.72 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 5767 helix: 1.57 (0.11), residues: 2029 sheet: 0.00 (0.15), residues: 1108 loop : 0.02 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP d 9 HIS 0.014 0.001 HIS c 33 PHE 0.029 0.002 PHE d 68 TYR 0.033 0.002 TYR i 94 ARG 0.013 0.001 ARG r 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1408 time to evaluate : 6.703 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: K 54 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8596 (tttm) REVERT: Q 94 MET cc_start: 0.7538 (mmt) cc_final: 0.7237 (mmt) REVERT: T 46 ILE cc_start: 0.7943 (mp) cc_final: 0.7699 (mp) REVERT: f 13 ASN cc_start: 0.6053 (p0) cc_final: 0.5844 (p0) REVERT: t 17 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6682 (mtt-85) REVERT: e 43 ASN cc_start: 0.7878 (t0) cc_final: 0.7429 (t0) REVERT: h 69 ASN cc_start: 0.8221 (p0) cc_final: 0.7593 (p0) REVERT: h 99 ASN cc_start: 0.7756 (t0) cc_final: 0.7485 (t0) REVERT: h 110 GLN cc_start: 0.7655 (mp10) cc_final: 0.7142 (mp10) REVERT: m 110 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7593 (mttt) outliers start: 247 outliers final: 146 residues processed: 1502 average time/residue: 1.7922 time to fit residues: 4042.2349 Evaluate side-chains 1504 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1356 time to evaluate : 7.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 95 GLN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 41 ASN Chi-restraints excluded: chain Y residue 8 ASP Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 17 ARG Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 100 ARG Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 7.9990 chunk 887 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 578 optimal weight: 40.0000 chunk 243 optimal weight: 20.0000 chunk 986 optimal weight: 5.9990 chunk 819 optimal weight: 20.0000 chunk 456 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 518 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN M 123 HIS N 68 ASN Q 108 GLN S 28 GLN U 59 GLN X 41 ASN 1 4 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN p 88 GLN t 84 ASN d 64 ASN d 67 GLN d 190 ASN e 93 ASN l 59 ASN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 GLN ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 136 GLN g 129 ASN i 126 GLN j 64 GLN n 19 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 463 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 157094 Z= 0.272 Angle : 0.595 17.283 234769 Z= 0.307 Chirality : 0.035 0.319 29928 Planarity : 0.004 0.128 12676 Dihedral : 23.352 179.535 78032 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 4.16 % Allowed : 25.68 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5767 helix: 1.55 (0.12), residues: 2032 sheet: 0.03 (0.15), residues: 1138 loop : 0.06 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 9 136 HIS 0.011 0.001 HIS c 33 PHE 0.031 0.002 PHE d 68 TYR 0.033 0.002 TYR i 94 ARG 0.016 0.001 ARG J 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1437 time to evaluate : 6.668 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: K 4 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: K 54 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8562 (tttm) REVERT: Q 94 MET cc_start: 0.7498 (mmt) cc_final: 0.7187 (mmt) REVERT: T 46 ILE cc_start: 0.7947 (mp) cc_final: 0.7705 (mp) REVERT: e 43 ASN cc_start: 0.7788 (t0) cc_final: 0.7358 (t0) REVERT: h 69 ASN cc_start: 0.8191 (p0) cc_final: 0.7708 (p0) REVERT: h 99 ASN cc_start: 0.7683 (t0) cc_final: 0.7453 (t0) REVERT: h 110 GLN cc_start: 0.7625 (mp10) cc_final: 0.7181 (mp10) REVERT: k 100 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7242 (mpp80) REVERT: q 52 ASN cc_start: 0.7635 (m-40) cc_final: 0.7363 (m110) REVERT: i 67 VAL cc_start: 0.7988 (p) cc_final: 0.7605 (p) REVERT: i 75 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6095 (mt0) outliers start: 206 outliers final: 132 residues processed: 1515 average time/residue: 1.7013 time to fit residues: 3859.8763 Evaluate side-chains 1504 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1368 time to evaluate : 6.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain S residue 95 GLN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 41 ASN Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 GLN Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 68 GLN Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 100 ARG Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain 9 residue 141 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 562 optimal weight: 0.0270 chunk 720 optimal weight: 20.0000 chunk 558 optimal weight: 5.9990 chunk 830 optimal weight: 20.0000 chunk 551 optimal weight: 9.9990 chunk 983 optimal weight: 5.9990 chunk 615 optimal weight: 5.9990 chunk 599 optimal weight: 10.0000 chunk 453 optimal weight: 6.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN N 68 ASN Q 108 GLN R 18 GLN S 28 GLN U 59 GLN X 41 ASN b 103 ASN 1 4 ASN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN e 70 ASN e 93 ASN l 59 ASN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 GLN ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 133 GLN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 ASN g 86 GLN g 129 ASN i 32 ASN i 126 GLN j 64 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 260 GLN 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 157094 Z= 0.213 Angle : 0.583 17.229 234769 Z= 0.301 Chirality : 0.033 0.288 29928 Planarity : 0.004 0.126 12676 Dihedral : 23.341 179.540 78030 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.78 % Allowed : 27.54 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 5767 helix: 1.53 (0.12), residues: 2022 sheet: 0.02 (0.15), residues: 1145 loop : 0.09 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 9 136 HIS 0.010 0.001 HIS c 33 PHE 0.031 0.001 PHE d 68 TYR 0.036 0.002 TYR j 58 ARG 0.017 0.000 ARG k 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1450 time to evaluate : 6.578 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: G 95 TYR cc_start: 0.6891 (m-10) cc_final: 0.6472 (m-10) REVERT: K 54 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8540 (tttm) REVERT: T 46 ILE cc_start: 0.7965 (mp) cc_final: 0.7695 (mp) REVERT: f 74 GLU cc_start: 0.5186 (tp30) cc_final: 0.4953 (tp30) REVERT: d 127 ASP cc_start: 0.6414 (p0) cc_final: 0.6173 (p0) REVERT: e 43 ASN cc_start: 0.7731 (t0) cc_final: 0.7336 (t0) REVERT: h 68 GLN cc_start: 0.7389 (pp30) cc_final: 0.6814 (pp30) REVERT: h 69 ASN cc_start: 0.8182 (p0) cc_final: 0.7618 (p0) REVERT: h 99 ASN cc_start: 0.7673 (t0) cc_final: 0.7471 (t0) REVERT: h 110 GLN cc_start: 0.7642 (mp10) cc_final: 0.7161 (mp10) REVERT: i 67 VAL cc_start: 0.8011 (p) cc_final: 0.7631 (p) REVERT: i 75 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6074 (mt0) outliers start: 187 outliers final: 134 residues processed: 1520 average time/residue: 1.8527 time to fit residues: 4227.8275 Evaluate side-chains 1508 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1372 time to evaluate : 6.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 52 ASP Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 ASP Chi-restraints excluded: chain Y residue 54 LYS Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 23 LYS Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain 4 residue 22 LYS Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 58 LYS Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 69 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain 9 residue 141 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 6.9990 chunk 392 optimal weight: 20.0000 chunk 587 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 625 optimal weight: 7.9990 chunk 669 optimal weight: 8.9990 chunk 486 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 772 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN K 4 GLN K 45 GLN K 109 ASN N 68 ASN Q 108 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN S 95 GLN U 59 GLN X 16 ASN b 103 ASN 1 4 ASN d 64 ASN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN e 93 ASN k 66 GLN ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 GLN c 125 ASN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN g 129 ASN i 126 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN 9 298 ASN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 157094 Z= 0.301 Angle : 0.611 17.224 234769 Z= 0.314 Chirality : 0.035 0.374 29928 Planarity : 0.005 0.129 12676 Dihedral : 23.290 179.751 78030 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.86 % Allowed : 28.32 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.11), residues: 5767 helix: 1.43 (0.12), residues: 2025 sheet: 0.05 (0.15), residues: 1139 loop : 0.10 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 9 136 HIS 0.010 0.001 HIS c 33 PHE 0.052 0.002 PHE d 68 TYR 0.043 0.002 TYR j 58 ARG 0.019 0.001 ARG J 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1397 time to evaluate : 6.646 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: G 95 TYR cc_start: 0.7031 (m-10) cc_final: 0.6680 (m-10) REVERT: K 54 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8561 (tttm) REVERT: T 46 ILE cc_start: 0.7935 (mp) cc_final: 0.7666 (mp) REVERT: f 53 ASN cc_start: 0.7600 (p0) cc_final: 0.7359 (p0) REVERT: p 14 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7732 (mmmm) REVERT: p 52 ASP cc_start: 0.6715 (t0) cc_final: 0.6195 (OUTLIER) REVERT: e 43 ASN cc_start: 0.7777 (t0) cc_final: 0.7380 (t0) REVERT: h 69 ASN cc_start: 0.8236 (p0) cc_final: 0.7662 (p0) REVERT: h 110 GLN cc_start: 0.7676 (mp10) cc_final: 0.7204 (mp10) REVERT: i 67 VAL cc_start: 0.8042 (p) cc_final: 0.7582 (p) REVERT: i 75 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6118 (mt0) REVERT: s 21 LYS cc_start: 0.7136 (mmpt) cc_final: 0.6795 (mmpt) outliers start: 191 outliers final: 142 residues processed: 1469 average time/residue: 1.8833 time to fit residues: 4152.2129 Evaluate side-chains 1490 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1347 time to evaluate : 6.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Y residue 8 ASP Chi-restraints excluded: chain Y residue 54 LYS Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 SER Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain 4 residue 22 LYS Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 73 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 68 GLN Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain 9 residue 141 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 3.9990 chunk 941 optimal weight: 20.0000 chunk 859 optimal weight: 6.9990 chunk 916 optimal weight: 7.9990 chunk 551 optimal weight: 9.9990 chunk 399 optimal weight: 6.9990 chunk 719 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 827 optimal weight: 20.0000 chunk 866 optimal weight: 0.6980 chunk 912 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 75 ASN K 109 ASN N 68 ASN S 28 GLN 1 4 ASN 3 40 GLN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 70 ASN e 93 ASN k 66 GLN l 125 GLN c 125 ASN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 GLN g 129 ASN i 126 GLN m 76 ASN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 157094 Z= 0.219 Angle : 0.601 17.175 234769 Z= 0.309 Chirality : 0.034 0.318 29928 Planarity : 0.004 0.125 12676 Dihedral : 23.322 179.476 78030 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 3.33 % Allowed : 29.41 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 5767 helix: 1.41 (0.12), residues: 2011 sheet: 0.03 (0.15), residues: 1143 loop : 0.11 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 9 136 HIS 0.009 0.001 HIS c 33 PHE 0.048 0.002 PHE d 68 TYR 0.043 0.002 TYR j 58 ARG 0.019 0.001 ARG k 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1416 time to evaluate : 6.757 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: G 95 TYR cc_start: 0.7037 (m-10) cc_final: 0.6750 (m-10) REVERT: K 4 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7456 (tm-30) REVERT: N 73 GLU cc_start: 0.7367 (pm20) cc_final: 0.5935 (pm20) REVERT: O 2 ILE cc_start: 0.8145 (tp) cc_final: 0.7941 (tp) REVERT: R 1 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6977 (ptm) REVERT: T 46 ILE cc_start: 0.7831 (mp) cc_final: 0.7592 (mp) REVERT: 0 7 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7721 (ptp-170) REVERT: e 43 ASN cc_start: 0.7748 (t0) cc_final: 0.7357 (t0) REVERT: h 69 ASN cc_start: 0.8237 (p0) cc_final: 0.7642 (p0) REVERT: h 110 GLN cc_start: 0.7697 (mp10) cc_final: 0.7227 (mp10) REVERT: i 67 VAL cc_start: 0.7993 (p) cc_final: 0.7631 (p) REVERT: i 75 GLN cc_start: 0.6423 (OUTLIER) cc_final: 0.6054 (mt0) outliers start: 165 outliers final: 123 residues processed: 1482 average time/residue: 1.8650 time to fit residues: 4151.4960 Evaluate side-chains 1496 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1370 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 16 ARG Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Y residue 15 GLU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 0 residue 7 ARG Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain 4 residue 22 LYS Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 68 GLN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 20.0000 chunk 968 optimal weight: 0.8980 chunk 591 optimal weight: 10.0000 chunk 459 optimal weight: 5.9990 chunk 673 optimal weight: 3.9990 chunk 1016 optimal weight: 6.9990 chunk 935 optimal weight: 3.9990 chunk 809 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 625 optimal weight: 9.9990 chunk 496 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN K 45 GLN N 68 ASN N 76 ASN R 18 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN S 95 GLN U 59 GLN 1 4 ASN ** f 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 ASN k 66 GLN c 61 ASN c 125 ASN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN g 129 ASN i 32 ASN i 126 GLN m 76 ASN 9 286 GLN ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 157094 Z= 0.204 Angle : 0.603 17.145 234769 Z= 0.309 Chirality : 0.033 0.323 29928 Planarity : 0.005 0.124 12676 Dihedral : 23.296 179.490 78030 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 2.83 % Allowed : 30.44 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5767 helix: 1.32 (0.12), residues: 2010 sheet: 0.06 (0.15), residues: 1161 loop : 0.09 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 9 136 HIS 0.009 0.001 HIS c 33 PHE 0.047 0.002 PHE d 68 TYR 0.039 0.002 TYR j 58 ARG 0.022 0.001 ARG J 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1420 time to evaluate : 6.657 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: G 95 TYR cc_start: 0.7046 (m-10) cc_final: 0.6813 (m-10) REVERT: R 1 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6915 (ptm) REVERT: T 46 ILE cc_start: 0.7841 (mp) cc_final: 0.7632 (mp) REVERT: 0 7 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (ptp-170) REVERT: t 32 ILE cc_start: 0.8104 (mm) cc_final: 0.7647 (mp) REVERT: d 190 ASN cc_start: 0.6617 (t0) cc_final: 0.6125 (t160) REVERT: e 43 ASN cc_start: 0.7725 (t0) cc_final: 0.7337 (t0) REVERT: h 68 GLN cc_start: 0.7355 (pp30) cc_final: 0.6937 (pp30) REVERT: h 69 ASN cc_start: 0.8195 (p0) cc_final: 0.7425 (p0) REVERT: h 91 SER cc_start: 0.7595 (m) cc_final: 0.7283 (m) REVERT: h 110 GLN cc_start: 0.7706 (mp10) cc_final: 0.7246 (mp10) REVERT: i 67 VAL cc_start: 0.8008 (p) cc_final: 0.7617 (p) REVERT: i 75 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6024 (mt0) REVERT: j 7 ARG cc_start: 0.7331 (ttm170) cc_final: 0.7015 (ttm170) REVERT: j 71 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7082 (mtpt) outliers start: 140 outliers final: 113 residues processed: 1477 average time/residue: 1.8553 time to fit residues: 4119.5256 Evaluate side-chains 1494 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1378 time to evaluate : 6.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 118 ASN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 10 THR Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain 0 residue 7 ARG Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 54 ASP Chi-restraints excluded: chain 3 residue 64 ASN Chi-restraints excluded: chain 4 residue 22 LYS Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain m residue 12 ASP Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 60 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain 9 residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 5.9990 chunk 861 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 810 optimal weight: 30.0000 chunk 339 optimal weight: 5.9990 chunk 832 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 48 HIS N 68 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN U 58 ASN 1 4 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN e 70 ASN e 93 ASN ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN ** o 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 GLN 9 292 HIS ** 9 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 463 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.032420 restraints weight = 605082.825| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 1.55 r_work: 0.2323 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2230 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 157094 Z= 0.432 Angle : 0.669 17.278 234769 Z= 0.344 Chirality : 0.039 0.356 29928 Planarity : 0.005 0.132 12676 Dihedral : 23.235 179.562 78028 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 2.87 % Allowed : 30.67 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.11), residues: 5767 helix: 1.22 (0.12), residues: 2020 sheet: 0.02 (0.15), residues: 1157 loop : 0.07 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP 9 136 HIS 0.011 0.001 HIS c 33 PHE 0.041 0.002 PHE d 68 TYR 0.044 0.002 TYR j 58 ARG 0.023 0.001 ARG k 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57995.00 seconds wall clock time: 1002 minutes 6.81 seconds (60126.81 seconds total)