Starting phenix.real_space_refine on Sun Sep 29 03:48:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/09_2024/6ff4_4255.cif" } resolution = 3.4 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= 0.007 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 282 5.49 5 Mg 4 5.21 5 S 339 5.16 5 C 44960 2.51 5 N 12625 2.21 5 O 14172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72392 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "2" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1262 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 19, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 48} Chain breaks: 2 Chain: "3" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 981 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "5" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1470 Classifications: {'RNA': 70} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 36} Link IDs: {'rna2p': 16, 'rna3p': 53} Chain: "6" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2035 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 34} Link IDs: {'rna2p': 14, 'rna3p': 80} Chain: "7" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "8" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1211 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 9, 'TRANS': 134} Chain: "A" Number of atoms: 18569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2238, 18569 Classifications: {'peptide': 2238} Link IDs: {'PCIS': 1, 'PTRANS': 125, 'TRANS': 2111} Chain breaks: 2 Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 55, 'TRANS': 846} Chain: "C" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2287 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 19, 'TRANS': 266} Chain breaks: 1 Chain: "D" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2517 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Chain: "E" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1054 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain breaks: 1 Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "O" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2235 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 3, 'TRANS': 249} Chain: "P" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2305 Classifications: {'peptide': 286} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 1 Chain: "Q" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1153 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 130} Chain: "R" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 869 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain breaks: 1 Chain: "S" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 261 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "V" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 762 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "Z" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1013 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 14, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 35} Chain breaks: 1 Chain: "s" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1377 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "t" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1415 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 2 Chain: "u" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 7013 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 1 Chain: "v" Number of atoms: 9315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9315 Classifications: {'peptide': 1189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 58, 'TRANS': 1127} Chain breaks: 4 Chain: "x" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 656 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "y" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 766 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "z" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 839 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43414 SG CYS P 24 50.953 74.167 65.199 1.00 41.59 S ATOM 43436 SG CYS P 27 49.863 77.360 66.381 1.00 41.94 S ATOM 43879 SG CYS P 81 53.773 74.914 67.691 1.00 46.73 S ATOM 43901 SG CYS P 84 50.445 74.668 68.727 1.00 47.23 S ATOM 44547 SG CYS P 165 36.296 90.945 78.391 1.00 58.25 S ATOM 44613 SG CYS P 173 34.621 95.389 77.896 1.00 58.03 S ATOM 44661 SG CYS P 179 36.261 93.192 75.546 1.00 53.98 S ATOM 43585 SG CYS P 45 63.006 79.513 74.280 1.00 45.52 S ATOM 43608 SG CYS P 48 66.538 79.166 74.994 1.00 45.69 S ATOM 43804 SG CYS P 71 65.447 78.780 70.799 1.00 43.75 S ATOM 43826 SG CYS P 74 65.118 76.281 73.385 1.00 43.70 S ATOM 46486 SG CYS Q 101 40.670 109.804 60.592 1.00 39.22 S ATOM 46492 SG CYS Q 102 44.149 112.736 62.950 1.00 36.50 S ATOM 46767 SG CYS Q 137 43.100 109.415 63.230 1.00 32.19 S ATOM 46486 SG CYS Q 101 40.670 109.804 60.592 1.00 39.22 S ATOM 46625 SG CYS Q 119 38.412 106.994 60.263 1.00 37.25 S ATOM 46517 SG CYS Q 105 42.936 107.048 60.714 1.00 28.89 S ATOM 46611 SG CYS Q 117 42.917 103.370 61.047 1.00 32.48 S ATOM 46744 SG CYS Q 134 42.156 105.455 63.861 1.00 33.57 S ATOM 53022 SG CYS t 202 87.501 107.541 114.162 1.00 18.13 S ATOM 53097 SG CYS t 211 90.287 105.137 114.991 1.00 20.91 S ATOM 53136 SG CYS t 217 90.646 109.082 114.676 1.00 17.46 S ATOM 70787 SG CYS y 11 103.838 97.988 173.098 1.00 17.72 S ATOM 71050 SG CYS y 46 101.346 100.583 174.992 1.00 17.87 S ATOM 71073 SG CYS y 49 103.454 101.281 171.835 1.00 21.41 S ATOM 71344 SG CYS y 85 100.267 97.860 172.921 1.00 17.85 S ATOM 70874 SG CYS y 23 97.863 104.289 157.105 1.00 23.88 S ATOM 70898 SG CYS y 26 98.064 100.805 155.928 1.00 23.69 S ATOM 71145 SG CYS y 58 98.400 103.089 160.489 1.00 23.30 S ATOM 71166 SG CYS y 61 101.024 102.504 156.776 1.00 25.80 S ATOM 70925 SG CYS y 30 92.594 91.888 161.724 1.00 17.61 S ATOM 71241 SG CYS y 72 90.204 89.815 159.834 1.00 15.01 S ATOM 71265 SG CYS y 75 92.838 88.736 163.402 1.00 15.43 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASN C 413 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 413 " occ=0.00 residue: pdb=" N GLN C 414 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN C 414 " occ=0.00 residue: pdb=" N SER C 415 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER C 415 " occ=0.00 Time building chain proxies: 29.36, per 1000 atoms: 0.41 Number of scatterers: 72392 At special positions: 0 Unit cell: (193.72, 207.64, 251.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 339 16.00 P 282 15.00 Mg 4 11.99 O 14172 8.00 N 12625 7.00 C 44960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 56 " - pdb=" SG CYS 7 59 " distance=2.03 Simple disulfide: pdb=" SG CYS s 44 " - pdb=" SG CYS s 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.07 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 501 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 27 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 81 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 84 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 24 " pdb=" ZN P 502 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 173 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 179 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 165 " pdb=" ZN P 503 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 71 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 48 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 45 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 74 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 137 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 101 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 102 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 119 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 101 " pdb=" ZN Q 203 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 105 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 117 " pdb=" ZN t 401 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 202 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 211 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 217 " pdb=" ZN y 201 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 46 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 49 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 85 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 11 " pdb=" ZN y 202 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 23 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 26 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 61 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 58 " pdb=" ZN y 203 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 75 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 30 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 72 " Number of angles added : 24 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15506 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 64 sheets defined 38.0% alpha, 12.3% beta 64 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 20.45 Creating SS restraints... Processing helix chain '1' and resid 4 through 21 removed outlier: 3.773A pdb=" N LYS 1 8 " --> pdb=" O LEU 1 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN 1 14 " --> pdb=" O ILE 1 10 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 57 Processing helix chain '1' and resid 58 through 60 No H-bonds generated for 'chain '1' and resid 58 through 60' Processing helix chain '1' and resid 86 through 97 removed outlier: 3.745A pdb=" N THR 1 90 " --> pdb=" O ASP 1 86 " (cutoff:3.500A) Processing helix chain '3' and resid 501 through 519 removed outlier: 4.161A pdb=" N GLN 3 519 " --> pdb=" O MET 3 515 " (cutoff:3.500A) Processing helix chain '3' and resid 530 through 535 Processing helix chain '3' and resid 536 through 538 No H-bonds generated for 'chain '3' and resid 536 through 538' Processing helix chain '3' and resid 545 through 550 removed outlier: 3.674A pdb=" N ILE 3 549 " --> pdb=" O MET 3 545 " (cutoff:3.500A) Processing helix chain '3' and resid 593 through 616 removed outlier: 3.767A pdb=" N GLU 3 609 " --> pdb=" O LYS 3 605 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS 3 613 " --> pdb=" O GLU 3 609 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 42 Processing helix chain '7' and resid 65 through 70 Processing helix chain '7' and resid 81 through 90 removed outlier: 4.101A pdb=" N ARG 7 85 " --> pdb=" O ASN 7 81 " (cutoff:3.500A) Processing helix chain '8' and resid 461 through 469 removed outlier: 3.685A pdb=" N VAL 8 469 " --> pdb=" O LEU 8 465 " (cutoff:3.500A) Processing helix chain '8' and resid 478 through 482 Processing helix chain '8' and resid 484 through 492 Processing helix chain '8' and resid 501 through 505 removed outlier: 3.633A pdb=" N TRP 8 504 " --> pdb=" O PRO 8 501 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS 8 505 " --> pdb=" O ARG 8 502 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 501 through 505' Processing helix chain '8' and resid 525 through 530 Processing helix chain '8' and resid 532 through 545 Processing helix chain '8' and resid 548 through 555 Processing helix chain '8' and resid 568 through 577 Processing helix chain 'A' and resid 28 through 45 removed outlier: 4.791A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 81 through 91 removed outlier: 3.531A pdb=" N LYS A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.522A pdb=" N LYS A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 removed outlier: 3.566A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.358A pdb=" N ASP A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.805A pdb=" N LEU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.616A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.558A pdb=" N ILE A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.961A pdb=" N ASN A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 413' Processing helix chain 'A' and resid 440 through 460 removed outlier: 4.002A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.986A pdb=" N ALA A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 511 removed outlier: 4.177A pdb=" N LEU A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 566 removed outlier: 3.589A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.816A pdb=" N HIS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 662 removed outlier: 4.284A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 677 through 694 removed outlier: 3.739A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 removed outlier: 3.563A pdb=" N GLN A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 removed outlier: 3.644A pdb=" N TYR A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 796 removed outlier: 3.768A pdb=" N GLY A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 4.121A pdb=" N VAL A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 848 removed outlier: 4.054A pdb=" N LEU A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 Processing helix chain 'A' and resid 873 through 887 removed outlier: 3.665A pdb=" N LYS A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 933 removed outlier: 4.148A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 952 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 989 through 997 Processing helix chain 'A' and resid 1002 through 1012 removed outlier: 4.092A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1077 through 1082 removed outlier: 3.743A pdb=" N ALA A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1114 Processing helix chain 'A' and resid 1143 through 1159 removed outlier: 3.542A pdb=" N ASN A1159 " --> pdb=" O TRP A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1202 No H-bonds generated for 'chain 'A' and resid 1200 through 1202' Processing helix chain 'A' and resid 1233 through 1250 removed outlier: 3.544A pdb=" N MET A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1253 No H-bonds generated for 'chain 'A' and resid 1251 through 1253' Processing helix chain 'A' and resid 1255 through 1272 removed outlier: 3.567A pdb=" N ILE A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 4.171A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1281' Processing helix chain 'A' and resid 1281 through 1303 removed outlier: 3.509A pdb=" N LEU A1287 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A1293 " --> pdb=" O VAL A1289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 4.618A pdb=" N LYS A1344 " --> pdb=" O LEU A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.576A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1440 through 1446 removed outlier: 3.717A pdb=" N GLN A1446 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1462 removed outlier: 3.618A pdb=" N ASP A1461 " --> pdb=" O HIS A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1479 removed outlier: 4.340A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1525 Processing helix chain 'A' and resid 1527 through 1538 removed outlier: 4.310A pdb=" N ASN A1531 " --> pdb=" O ASN A1527 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A1535 " --> pdb=" O ASN A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1573 removed outlier: 3.713A pdb=" N LYS A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1596 Processing helix chain 'A' and resid 1597 through 1599 No H-bonds generated for 'chain 'A' and resid 1597 through 1599' Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.573A pdb=" N ARG A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1736 removed outlier: 3.802A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1733 " --> pdb=" O ALA A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1750 removed outlier: 4.212A pdb=" N ARG A1744 " --> pdb=" O LEU A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1827 removed outlier: 3.741A pdb=" N VAL A1826 " --> pdb=" O HIS A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1835 Processing helix chain 'A' and resid 1836 through 1852 removed outlier: 4.281A pdb=" N ALA A1842 " --> pdb=" O LYS A1838 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A1843 " --> pdb=" O TRP A1839 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A1844 " --> pdb=" O LYS A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1876 Processing helix chain 'A' and resid 1892 through 1898 Processing helix chain 'A' and resid 1899 through 1908 removed outlier: 3.842A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 removed outlier: 3.899A pdb=" N LEU A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1946 through 1954 Processing helix chain 'A' and resid 1972 through 1995 Processing helix chain 'A' and resid 2003 through 2012 Processing helix chain 'A' and resid 2068 through 2077 removed outlier: 3.707A pdb=" N GLU A2072 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A2074 " --> pdb=" O LYS A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2087 Processing helix chain 'A' and resid 2107 through 2117 Processing helix chain 'A' and resid 2189 through 2203 Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2254 No H-bonds generated for 'chain 'A' and resid 2252 through 2254' Processing helix chain 'A' and resid 2284 through 2288 removed outlier: 3.876A pdb=" N HIS A2288 " --> pdb=" O GLY A2285 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.935A pdb=" N ALA B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.775A pdb=" N ASP B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.823A pdb=" N GLU B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 220 removed outlier: 4.217A pdb=" N VAL B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 270 through 290 Processing helix chain 'B' and resid 319 through 329 removed outlier: 4.481A pdb=" N LYS B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.888A pdb=" N LEU B 343 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.535A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.891A pdb=" N VAL B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.950A pdb=" N LYS B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 599 through 614 removed outlier: 4.082A pdb=" N MET B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 647 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 722 Processing helix chain 'B' and resid 725 through 730 removed outlier: 4.086A pdb=" N ARG B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 740 Processing helix chain 'B' and resid 764 through 775 removed outlier: 3.856A pdb=" N ARG B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 822 Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.953A pdb=" N TYR B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 880 No H-bonds generated for 'chain 'B' and resid 878 through 880' Processing helix chain 'B' and resid 882 through 891 Processing helix chain 'B' and resid 928 through 939 removed outlier: 3.924A pdb=" N GLU B 932 " --> pdb=" O HIS B 928 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B 937 " --> pdb=" O PHE B 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.585A pdb=" N ALA C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 removed outlier: 4.158A pdb=" N TYR C 113 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 115 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR C 116 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR C 117 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 118 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 136 through 163 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 282 through 326 removed outlier: 3.685A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 463 removed outlier: 4.088A pdb=" N SER D 463 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 90 removed outlier: 3.921A pdb=" N MET E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 156 through 162 removed outlier: 3.967A pdb=" N GLU E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 220 Processing helix chain 'L' and resid 12 through 26 removed outlier: 4.193A pdb=" N ILE L 18 " --> pdb=" O THR L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 36 Processing helix chain 'L' and resid 42 through 53 Processing helix chain 'L' and resid 65 through 72 Processing helix chain 'L' and resid 85 through 90 Processing helix chain 'L' and resid 95 through 108 Processing helix chain 'O' and resid 216 through 238 Processing helix chain 'O' and resid 242 through 254 Processing helix chain 'O' and resid 260 through 267 Processing helix chain 'O' and resid 275 through 289 removed outlier: 4.060A pdb=" N TRP O 279 " --> pdb=" O ASN O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 291 through 306 removed outlier: 4.525A pdb=" N ARG O 301 " --> pdb=" O ASN O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 323 removed outlier: 4.306A pdb=" N TRP O 313 " --> pdb=" O VAL O 309 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 339 removed outlier: 3.826A pdb=" N TRP O 339 " --> pdb=" O ARG O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 355 removed outlier: 3.568A pdb=" N TRP O 346 " --> pdb=" O GLU O 342 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER O 348 " --> pdb=" O GLN O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 371 removed outlier: 3.637A pdb=" N ALA O 362 " --> pdb=" O GLU O 358 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR O 366 " --> pdb=" O ALA O 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU O 367 " --> pdb=" O ARG O 363 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG O 368 " --> pdb=" O THR O 364 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 370 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU O 371 " --> pdb=" O GLU O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 383 removed outlier: 3.613A pdb=" N LYS O 381 " --> pdb=" O LYS O 377 " (cutoff:3.500A) Processing helix chain 'O' and resid 391 through 405 removed outlier: 4.018A pdb=" N PHE O 405 " --> pdb=" O ARG O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 413 removed outlier: 3.753A pdb=" N GLU O 413 " --> pdb=" O HIS O 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 410 through 413' Processing helix chain 'O' and resid 414 through 426 removed outlier: 3.747A pdb=" N ALA O 418 " --> pdb=" O HIS O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 437 removed outlier: 4.732A pdb=" N ILE O 435 " --> pdb=" O ARG O 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 461 removed outlier: 4.196A pdb=" N LYS O 461 " --> pdb=" O ILE O 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 removed outlier: 3.721A pdb=" N LEU P 28 " --> pdb=" O CYS P 24 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY P 29 " --> pdb=" O GLN P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 29' Processing helix chain 'P' and resid 72 through 77 Processing helix chain 'P' and resid 93 through 101 removed outlier: 3.552A pdb=" N ARG P 97 " --> pdb=" O PRO P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 125 Processing helix chain 'P' and resid 135 through 139 removed outlier: 3.925A pdb=" N GLY P 138 " --> pdb=" O GLY P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.827A pdb=" N ALA P 151 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 160 removed outlier: 3.971A pdb=" N ARG P 159 " --> pdb=" O TYR P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 179 removed outlier: 3.950A pdb=" N CYS P 179 " --> pdb=" O GLY P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 218 removed outlier: 3.738A pdb=" N ALA P 210 " --> pdb=" O ASN P 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP P 211 " --> pdb=" O ASP P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 254 removed outlier: 3.722A pdb=" N GLN P 254 " --> pdb=" O ASN P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 287 removed outlier: 3.543A pdb=" N ALA P 283 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 35 Processing helix chain 'Q' and resid 46 through 65 removed outlier: 3.903A pdb=" N PHE Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 82 Processing helix chain 'Q' and resid 87 through 93 Processing helix chain 'Q' and resid 102 through 106 removed outlier: 3.574A pdb=" N ILE Q 106 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 121 removed outlier: 3.816A pdb=" N VAL Q 121 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 126 Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 60 through 71 Processing helix chain 'R' and resid 217 through 227 Processing helix chain 'V' and resid 32 through 45 removed outlier: 3.536A pdb=" N CYS V 36 " --> pdb=" O ALA V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 123 Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'Y' and resid 32 through 36 removed outlier: 3.729A pdb=" N GLU Y 35 " --> pdb=" O GLU Y 32 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS Y 36 " --> pdb=" O CYS Y 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 32 through 36' Processing helix chain 'Y' and resid 39 through 43 Processing helix chain 'Y' and resid 48 through 60 Processing helix chain 'Y' and resid 67 through 75 Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.542A pdb=" N MET Y 85 " --> pdb=" O ASP Y 81 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 115 Proline residue: Y 107 - end of helix removed outlier: 4.131A pdb=" N ASN Y 115 " --> pdb=" O SER Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 125 Processing helix chain 's' and resid 33 through 46 Processing helix chain 's' and resid 120 through 124 removed outlier: 3.663A pdb=" N ASN s 124 " --> pdb=" O ASP s 121 " (cutoff:3.500A) Processing helix chain 's' and resid 137 through 143 removed outlier: 3.622A pdb=" N MET s 141 " --> pdb=" O THR s 137 " (cutoff:3.500A) Processing helix chain 't' and resid 129 through 144 Processing helix chain 't' and resid 156 through 160 removed outlier: 3.862A pdb=" N TYR t 159 " --> pdb=" O ILE t 156 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN t 160 " --> pdb=" O ASN t 157 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 156 through 160' Processing helix chain 't' and resid 202 through 208 Processing helix chain 't' and resid 228 through 237 Processing helix chain 't' and resid 282 through 293 Processing helix chain 'u' and resid 400 through 408 Processing helix chain 'u' and resid 475 through 479 Processing helix chain 'u' and resid 492 through 494 No H-bonds generated for 'chain 'u' and resid 492 through 494' Processing helix chain 'u' and resid 495 through 507 removed outlier: 4.201A pdb=" N LYS u 499 " --> pdb=" O ARG u 495 " (cutoff:3.500A) Processing helix chain 'u' and resid 508 through 522 Processing helix chain 'u' and resid 522 through 527 Processing helix chain 'u' and resid 527 through 540 removed outlier: 3.753A pdb=" N LEU u 531 " --> pdb=" O GLY u 527 " (cutoff:3.500A) Proline residue: u 537 - end of helix Processing helix chain 'u' and resid 545 through 559 Processing helix chain 'u' and resid 570 through 579 removed outlier: 4.092A pdb=" N VAL u 577 " --> pdb=" O LYS u 573 " (cutoff:3.500A) Processing helix chain 'u' and resid 580 through 582 No H-bonds generated for 'chain 'u' and resid 580 through 582' Processing helix chain 'u' and resid 586 through 605 Processing helix chain 'u' and resid 606 through 614 removed outlier: 3.560A pdb=" N ARG u 614 " --> pdb=" O ILE u 610 " (cutoff:3.500A) Processing helix chain 'u' and resid 621 through 640 Processing helix chain 'u' and resid 640 through 653 removed outlier: 4.436A pdb=" N LEU u 644 " --> pdb=" O GLY u 640 " (cutoff:3.500A) Proline residue: u 646 - end of helix removed outlier: 3.657A pdb=" N LYS u 653 " --> pdb=" O LYS u 649 " (cutoff:3.500A) Processing helix chain 'u' and resid 657 through 675 removed outlier: 4.078A pdb=" N ARG u 661 " --> pdb=" O SER u 657 " (cutoff:3.500A) Processing helix chain 'u' and resid 676 through 681 removed outlier: 3.735A pdb=" N ILE u 679 " --> pdb=" O GLY u 676 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU u 680 " --> pdb=" O CYS u 677 " (cutoff:3.500A) Proline residue: u 681 - end of helix No H-bonds generated for 'chain 'u' and resid 676 through 681' Processing helix chain 'u' and resid 682 through 691 removed outlier: 4.409A pdb=" N ILE u 689 " --> pdb=" O SER u 685 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE u 690 " --> pdb=" O LEU u 686 " (cutoff:3.500A) Processing helix chain 'u' and resid 698 through 717 removed outlier: 3.904A pdb=" N THR u 717 " --> pdb=" O ALA u 713 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 724 Processing helix chain 'u' and resid 727 through 738 Processing helix chain 'u' and resid 740 through 754 Processing helix chain 'u' and resid 755 through 757 No H-bonds generated for 'chain 'u' and resid 755 through 757' Processing helix chain 'u' and resid 758 through 768 Processing helix chain 'u' and resid 769 through 776 Processing helix chain 'u' and resid 781 through 796 removed outlier: 4.080A pdb=" N LYS u 793 " --> pdb=" O LEU u 789 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN u 794 " --> pdb=" O LYS u 790 " (cutoff:3.500A) Processing helix chain 'u' and resid 802 through 810 Processing helix chain 'u' and resid 810 through 818 Processing helix chain 'u' and resid 821 through 826 removed outlier: 3.521A pdb=" N LEU u 825 " --> pdb=" O HIS u 821 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP u 826 " --> pdb=" O ARG u 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 821 through 826' Processing helix chain 'u' and resid 826 through 844 removed outlier: 3.776A pdb=" N GLN u 832 " --> pdb=" O ARG u 828 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU u 833 " --> pdb=" O ASN u 829 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU u 839 " --> pdb=" O ASP u 835 " (cutoff:3.500A) Processing helix chain 'u' and resid 845 through 854 removed outlier: 4.287A pdb=" N ILE u 849 " --> pdb=" O GLY u 845 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG u 852 " --> pdb=" O GLU u 848 " (cutoff:3.500A) Processing helix chain 'u' and resid 855 through 857 No H-bonds generated for 'chain 'u' and resid 855 through 857' Processing helix chain 'u' and resid 861 through 879 Processing helix chain 'u' and resid 888 through 902 Processing helix chain 'u' and resid 908 through 922 Processing helix chain 'u' and resid 925 through 927 No H-bonds generated for 'chain 'u' and resid 925 through 927' Processing helix chain 'u' and resid 928 through 940 Processing helix chain 'u' and resid 941 through 945 Processing helix chain 'u' and resid 948 through 959 Processing helix chain 'u' and resid 959 through 964 removed outlier: 4.311A pdb=" N LYS u 963 " --> pdb=" O ALA u 959 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR u 964 " --> pdb=" O VAL u 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 959 through 964' Processing helix chain 'u' and resid 968 through 981 removed outlier: 4.039A pdb=" N VAL u 976 " --> pdb=" O GLY u 972 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL u 977 " --> pdb=" O HIS u 973 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU u 980 " --> pdb=" O VAL u 976 " (cutoff:3.500A) Processing helix chain 'u' and resid 986 through 1004 removed outlier: 3.646A pdb=" N SER u 992 " --> pdb=" O GLU u 988 " (cutoff:3.500A) Processing helix chain 'u' and resid 1012 through 1015 Processing helix chain 'u' and resid 1016 through 1024 Proline residue: u1022 - end of helix Processing helix chain 'u' and resid 1028 through 1046 Processing helix chain 'u' and resid 1053 through 1059 Processing helix chain 'u' and resid 1071 through 1089 removed outlier: 3.894A pdb=" N VAL u1078 " --> pdb=" O ARG u1074 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN u1079 " --> pdb=" O ARG u1075 " (cutoff:3.500A) Processing helix chain 'u' and resid 1092 through 1100 Processing helix chain 'u' and resid 1109 through 1123 removed outlier: 4.000A pdb=" N ALA u1115 " --> pdb=" O CYS u1111 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS u1123 " --> pdb=" O VAL u1119 " (cutoff:3.500A) Processing helix chain 'u' and resid 1128 through 1135 Processing helix chain 'u' and resid 1136 through 1138 No H-bonds generated for 'chain 'u' and resid 1136 through 1138' Processing helix chain 'u' and resid 1140 through 1159 Processing helix chain 'u' and resid 1160 through 1164 removed outlier: 3.714A pdb=" N LYS u1163 " --> pdb=" O GLU u1160 " (cutoff:3.500A) Processing helix chain 'u' and resid 1165 through 1178 Proline residue: u1171 - end of helix removed outlier: 3.733A pdb=" N ASP u1175 " --> pdb=" O PRO u1171 " (cutoff:3.500A) Processing helix chain 'u' and resid 1181 through 1199 removed outlier: 3.513A pdb=" N ARG u1185 " --> pdb=" O ASP u1181 " (cutoff:3.500A) Processing helix chain 'u' and resid 1204 through 1216 removed outlier: 3.867A pdb=" N LEU u1208 " --> pdb=" O CYS u1204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN u1209 " --> pdb=" O GLU u1205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN u1213 " --> pdb=" O ASN u1209 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR u1214 " --> pdb=" O HIS u1210 " (cutoff:3.500A) Processing helix chain 'u' and resid 1217 through 1221 removed outlier: 4.078A pdb=" N PHE u1220 " --> pdb=" O PRO u1217 " (cutoff:3.500A) Processing helix chain 'u' and resid 1223 through 1242 removed outlier: 4.774A pdb=" N VAL u1239 " --> pdb=" O GLU u1235 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA u1240 " --> pdb=" O GLY u1236 " (cutoff:3.500A) Processing helix chain 'u' and resid 1242 through 1251 removed outlier: 3.574A pdb=" N MET u1246 " --> pdb=" O GLY u1242 " (cutoff:3.500A) Processing helix chain 'u' and resid 1258 through 1276 removed outlier: 4.116A pdb=" N VAL u1264 " --> pdb=" O LYS u1260 " (cutoff:3.500A) Processing helix chain 'u' and resid 1297 through 1302 removed outlier: 3.872A pdb=" N ASP u1301 " --> pdb=" O ARG u1297 " (cutoff:3.500A) Processing helix chain 'v' and resid 189 through 195 removed outlier: 3.580A pdb=" N ASP v 195 " --> pdb=" O GLU v 191 " (cutoff:3.500A) Processing helix chain 'v' and resid 429 through 432 removed outlier: 4.106A pdb=" N ARG v 432 " --> pdb=" O ARG v 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 429 through 432' Processing helix chain 'v' and resid 808 through 826 Processing helix chain 'v' and resid 836 through 845 Processing helix chain 'v' and resid 848 through 853 Processing helix chain 'v' and resid 1134 through 1152 removed outlier: 3.931A pdb=" N SER v1150 " --> pdb=" O MET v1146 " (cutoff:3.500A) Processing helix chain 'v' and resid 1159 through 1165 Processing helix chain 'v' and resid 1176 through 1180 Processing helix chain 'v' and resid 1181 through 1185 removed outlier: 3.787A pdb=" N MET v1185 " --> pdb=" O PHE v1182 " (cutoff:3.500A) Processing helix chain 'v' and resid 1186 through 1197 Processing helix chain 'v' and resid 1200 through 1216 removed outlier: 4.244A pdb=" N ILE v1211 " --> pdb=" O LYS v1207 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG v1212 " --> pdb=" O LEU v1208 " (cutoff:3.500A) Processing helix chain 'x' and resid 27 through 46 removed outlier: 3.572A pdb=" N TRP x 31 " --> pdb=" O THR x 27 " (cutoff:3.500A) Processing helix chain 'x' and resid 46 through 57 removed outlier: 3.893A pdb=" N LEU x 50 " --> pdb=" O HIS x 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA x 56 " --> pdb=" O TYR x 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU x 57 " --> pdb=" O PHE x 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 60 through 71 Processing helix chain 'y' and resid 51 through 55 removed outlier: 3.545A pdb=" N GLN y 55 " --> pdb=" O GLY y 52 " (cutoff:3.500A) Processing helix chain 'y' and resid 73 through 77 Processing helix chain 'z' and resid 32 through 41 removed outlier: 4.138A pdb=" N TYR z 36 " --> pdb=" O ALA z 32 " (cutoff:3.500A) Processing helix chain 'z' and resid 67 through 76 Processing sheet with id=AA1, first strand: chain '1' and resid 64 through 66 removed outlier: 3.925A pdb=" N CYS 1 80 " --> pdb=" O LEU 1 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '7' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 910 removed outlier: 3.565A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1085 through 1091 removed outlier: 5.766A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 3.674A pdb=" N MET A1189 " --> pdb=" O PHE A1192 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1551 through 1555 removed outlier: 7.297A pdb=" N GLN A1552 " --> pdb=" O ARG t 194 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP t 196 " --> pdb=" O GLN A1552 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN A1554 " --> pdb=" O ASP t 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1609 through 1611 removed outlier: 3.810A pdb=" N LEU A1702 " --> pdb=" O TYR A1715 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1716 " --> pdb=" O SER A1643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1637 through 1638 Processing sheet with id=AB3, first strand: chain 'A' and resid 1883 through 1886 removed outlier: 6.318A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1787 through 1788 removed outlier: 4.364A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2256 through 2258 removed outlier: 4.578A pdb=" N ILE A2213 " --> pdb=" O TYR A2228 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY A2130 " --> pdb=" O PRO A2174 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A2127 " --> pdb=" O ILE A2145 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A2145 " --> pdb=" O TYR A2127 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A2104 " --> pdb=" O LEU A2262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2256 through 2258 removed outlier: 4.578A pdb=" N ILE A2213 " --> pdb=" O TYR A2228 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY A2130 " --> pdb=" O PRO A2174 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A2127 " --> pdb=" O ILE A2145 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A2145 " --> pdb=" O TYR A2127 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N PHE A2270 " --> pdb=" O GLU A2141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A2143 " --> pdb=" O PHE A2270 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N MET A2272 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A2145 " --> pdb=" O MET A2272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2151 through 2152 Processing sheet with id=AB8, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.509A pdb=" N ILE B 80 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU D 196 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG D 490 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 478 " --> pdb=" O CYS D 468 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS D 468 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA D 480 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 132 through 134 removed outlier: 6.496A pdb=" N VAL B 132 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 227 through 230 removed outlier: 5.683A pdb=" N LEU B 227 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN B 258 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE B 229 " --> pdb=" O ASN B 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AC3, first strand: chain 'B' and resid 476 through 478 removed outlier: 4.184A pdb=" N GLN B 505 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 527 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 480 through 483 Processing sheet with id=AC5, first strand: chain 'B' and resid 618 through 621 removed outlier: 3.539A pdb=" N HIS B 627 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 618 through 621 removed outlier: 3.539A pdb=" N HIS B 627 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 659 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 663 through 666 removed outlier: 6.833A pdb=" N PHE B 874 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 857 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 663 through 666 removed outlier: 7.500A pdb=" N LEU B 827 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 906 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B 829 " --> pdb=" O TRP B 904 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP B 904 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 831 " --> pdb=" O HIS B 902 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 686 through 691 removed outlier: 6.843A pdb=" N THR B 686 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 746 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 791 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.905A pdb=" N TYR C 176 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 196 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N MET P 36 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG C 198 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS P 38 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 200 " --> pdb=" O LYS P 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 207 through 212 removed outlier: 4.684A pdb=" N CYS D 209 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 223 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 240 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP D 232 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 238 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 249 through 254 Processing sheet with id=AD4, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.562A pdb=" N ALA D 312 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 324 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP D 316 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 322 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 333 through 338 removed outlier: 3.940A pdb=" N ILE D 345 " --> pdb=" O TRP D 357 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 354 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR D 367 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU D 356 " --> pdb=" O ARG D 365 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 377 through 379 removed outlier: 3.645A pdb=" N ALA D 377 " --> pdb=" O GLY D 390 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 416 through 421 removed outlier: 6.631A pdb=" N GLY D 430 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU D 419 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 428 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.613A pdb=" N ALA E 138 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 262 through 264 removed outlier: 4.110A pdb=" N VAL P 236 " --> pdb=" O ALA P 270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 51 through 52 removed outlier: 3.745A pdb=" N THR V 51 " --> pdb=" O ILE V 159 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL V 24 " --> pdb=" O CYS V 133 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE V 128 " --> pdb=" O MET V 100 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET V 100 " --> pdb=" O ILE V 128 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY V 96 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE V 97 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET V 61 " --> pdb=" O ILE V 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 52 through 53 removed outlier: 4.107A pdb=" N THR s 52 " --> pdb=" O ILE s 161 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS s 18 " --> pdb=" O LYS s 162 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS s 164 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU s 16 " --> pdb=" O CYS s 164 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE s 129 " --> pdb=" O MET s 101 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET s 101 " --> pdb=" O ILE s 129 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY s 131 " --> pdb=" O VAL s 99 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG s 56 " --> pdb=" O GLN s 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'u' and resid 412 through 413 removed outlier: 6.822A pdb=" N VAL z 63 " --> pdb=" O ARG z 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE z 48 " --> pdb=" O TYR z 61 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR z 61 " --> pdb=" O ILE z 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'v' and resid 1101 through 1107 removed outlier: 3.528A pdb=" N SER v1103 " --> pdb=" O THR v1120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR v1107 " --> pdb=" O SER v1116 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE v1126 " --> pdb=" O LEU v 8 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'v' and resid 16 through 20 removed outlier: 3.687A pdb=" N PHE v 16 " --> pdb=" O SER v 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU v 38 " --> pdb=" O THR v 55 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR v 55 " --> pdb=" O LEU v 38 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU v 40 " --> pdb=" O LEU v 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'v' and resid 62 through 69 removed outlier: 8.056A pdb=" N ASP v 76 " --> pdb=" O TYR v 92 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR v 92 " --> pdb=" O ASP v 76 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER v 82 " --> pdb=" O ARG v 86 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ARG v 86 " --> pdb=" O SER v 82 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE v 87 " --> pdb=" O GLN v 104 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN v 104 " --> pdb=" O ILE v 87 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE v 89 " --> pdb=" O ILE v 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'v' and resid 120 through 123 Processing sheet with id=AE8, first strand: chain 'v' and resid 120 through 123 Processing sheet with id=AE9, first strand: chain 'v' and resid 165 through 173 removed outlier: 6.661A pdb=" N LEU v 185 " --> pdb=" O TYR v 168 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL v 170 " --> pdb=" O ALA v 183 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA v 183 " --> pdb=" O VAL v 170 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY v 172 " --> pdb=" O MET v 181 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N MET v 181 " --> pdb=" O GLY v 172 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU v 208 " --> pdb=" O SER v 225 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER v 225 " --> pdb=" O LEU v 208 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE v 210 " --> pdb=" O LYS v 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS v 219 " --> pdb=" O ASP v 214 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'v' and resid 232 through 238 removed outlier: 3.972A pdb=" N PHE v 234 " --> pdb=" O CYS v 251 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY v 247 " --> pdb=" O VAL v 238 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'v' and resid 273 through 274 removed outlier: 7.105A pdb=" N ARG v 273 " --> pdb=" O PHE v 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'v' and resid 287 through 289 removed outlier: 6.745A pdb=" N GLN v 304 " --> pdb=" O VAL v 288 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE v 299 " --> pdb=" O LEU v 315 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU v 315 " --> pdb=" O PHE v 299 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP v 309 " --> pdb=" O THR v 305 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE v 310 " --> pdb=" O PHE v 330 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'v' and resid 292 through 294 removed outlier: 6.563A pdb=" N PHE v 299 " --> pdb=" O LEU v 315 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU v 315 " --> pdb=" O PHE v 299 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP v 309 " --> pdb=" O THR v 305 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU v 316 " --> pdb=" O GLU v 324 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU v 324 " --> pdb=" O GLU v 316 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE v 373 " --> pdb=" O LEU v 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'v' and resid 336 through 342 removed outlier: 3.985A pdb=" N ALA v 338 " --> pdb=" O ALA v 350 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN v 360 " --> pdb=" O LEU v 397 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU v 397 " --> pdb=" O GLN v 360 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'v' and resid 410 through 413 removed outlier: 3.650A pdb=" N ARG v 439 " --> pdb=" O ASN v 775 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'v' and resid 444 through 450 removed outlier: 6.826A pdb=" N ILE v 764 " --> pdb=" O MET v 447 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL v 449 " --> pdb=" O LEU v 762 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU v 762 " --> pdb=" O VAL v 449 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG v 763 " --> pdb=" O ALA v 756 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA v 756 " --> pdb=" O ARG v 763 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE v 757 " --> pdb=" O PHE v 741 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE v 741 " --> pdb=" O ILE v 757 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'v' and resid 458 through 462 removed outlier: 3.812A pdb=" N VAL v 462 " --> pdb=" O TYR v 473 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR v 473 " --> pdb=" O VAL v 462 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'v' and resid 507 through 510 Processing sheet with id=AG1, first strand: chain 'v' and resid 589 through 594 removed outlier: 4.293A pdb=" N ALA v 593 " --> pdb=" O PHE v 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE v 604 " --> pdb=" O ALA v 593 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE v 616 " --> pdb=" O LEU v 628 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER v 618 " --> pdb=" O GLN v 626 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN v 626 " --> pdb=" O SER v 618 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'v' and resid 672 through 675 Processing sheet with id=AG3, first strand: chain 'v' and resid 700 through 706 removed outlier: 3.681A pdb=" N VAL v 712 " --> pdb=" O SER v 722 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'v' and resid 785 through 791 removed outlier: 6.636A pdb=" N THR v 802 " --> pdb=" O PRO v 785 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS v 787 " --> pdb=" O ILE v 800 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN v 796 " --> pdb=" O HIS v 791 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'v' and resid 887 through 895 removed outlier: 5.632A pdb=" N ALA v 888 " --> pdb=" O ALA v 910 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA v 910 " --> pdb=" O ALA v 888 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER v 890 " --> pdb=" O GLY v 908 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'v' and resid 951 through 955 removed outlier: 3.839A pdb=" N ALA v 951 " --> pdb=" O GLY v 962 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL v 959 " --> pdb=" O TYR v 970 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'v' and resid 990 through 995 removed outlier: 3.530A pdb=" N GLY v 992 " --> pdb=" O SER v1003 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE v1009 " --> pdb=" O ASP v1026 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP v1026 " --> pdb=" O PHE v1009 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP v1011 " --> pdb=" O PHE v1024 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N GLN v1087 " --> pdb=" O ILE v1022 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE v1024 " --> pdb=" O GLN v1087 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA v1089 " --> pdb=" O PHE v1024 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP v1026 " --> pdb=" O ALA v1089 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL v1091 " --> pdb=" O ASP v1026 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL v1055 " --> pdb=" O ILE v1092 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN v1094 " --> pdb=" O ILE v1053 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE v1053 " --> pdb=" O ASN v1094 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN v1052 " --> pdb=" O ASP v1048 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP v1048 " --> pdb=" O ASN v1052 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR v1035 " --> pdb=" O ALA v1047 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'y' and resid 18 through 19 removed outlier: 3.981A pdb=" N ALA y 18 " --> pdb=" O ILE y 45 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'y' and resid 21 through 23 removed outlier: 6.184A pdb=" N LEU y 22 " --> pdb=" O VAL y 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'y' and resid 39 through 42 removed outlier: 6.491A pdb=" N TYR y 71 " --> pdb=" O CYS y 40 " (cutoff:3.500A) 2414 hydrogen bonds defined for protein. 6840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 155 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 41.43 Time building geometry restraints manager: 15.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 15652 1.33 - 1.45: 18441 1.45 - 1.57: 39415 1.57 - 1.69: 549 1.69 - 1.82: 535 Bond restraints: 74592 Sorted by residual: bond pdb=" C PRO z 14 " pdb=" N PRO z 15 " ideal model delta sigma weight residual 1.334 1.460 -0.126 2.34e-02 1.83e+03 2.90e+01 bond pdb=" C THR A 733 " pdb=" N PRO A 734 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.08e+01 bond pdb=" C ARG v1057 " pdb=" N LEU v1058 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.47e-02 4.63e+03 1.63e+01 bond pdb=" CB THR u1113 " pdb=" CG2 THR u1113 " ideal model delta sigma weight residual 1.521 1.401 0.120 3.30e-02 9.18e+02 1.32e+01 bond pdb=" O12 IHP A3001 " pdb=" P2 IHP A3001 " ideal model delta sigma weight residual 1.675 1.603 0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 74587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 97740 2.87 - 5.74: 3813 5.74 - 8.61: 544 8.61 - 11.48: 109 11.48 - 14.35: 35 Bond angle restraints: 102241 Sorted by residual: angle pdb=" C VAL R 201 " pdb=" N ASP R 202 " pdb=" CA ASP R 202 " ideal model delta sigma weight residual 126.45 138.70 -12.25 1.77e+00 3.19e-01 4.79e+01 angle pdb=" N GLY A1483 " pdb=" CA GLY A1483 " pdb=" C GLY A1483 " ideal model delta sigma weight residual 115.61 103.68 11.93 1.74e+00 3.30e-01 4.70e+01 angle pdb=" C VAL D 317 " pdb=" N ARG D 318 " pdb=" CA ARG D 318 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" N VAL 3 587 " pdb=" CA VAL 3 587 " pdb=" C VAL 3 587 " ideal model delta sigma weight residual 106.21 113.10 -6.89 1.07e+00 8.73e-01 4.15e+01 angle pdb=" C HIS E 146 " pdb=" N GLN E 147 " pdb=" CA GLN E 147 " ideal model delta sigma weight residual 121.54 133.72 -12.18 1.91e+00 2.74e-01 4.06e+01 ... (remaining 102236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 44172 35.04 - 70.08: 1116 70.08 - 105.12: 141 105.12 - 140.17: 12 140.17 - 175.21: 7 Dihedral angle restraints: 45448 sinusoidal: 21434 harmonic: 24014 Sorted by residual: dihedral pdb=" CA LYS B 352 " pdb=" C LYS B 352 " pdb=" N THR B 353 " pdb=" CA THR B 353 " ideal model delta harmonic sigma weight residual -180.00 -121.20 -58.80 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA SER v 584 " pdb=" C SER v 584 " pdb=" N ALA v 585 " pdb=" CA ALA v 585 " ideal model delta harmonic sigma weight residual -180.00 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS z 83 " pdb=" C CYS z 83 " pdb=" N ASN z 84 " pdb=" CA ASN z 84 " ideal model delta harmonic sigma weight residual -180.00 -126.54 -53.46 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 45445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 11352 0.965 - 1.931: 0 1.931 - 2.896: 0 2.896 - 3.861: 0 3.861 - 4.827: 4 Chirality restraints: 11356 Sorted by residual: chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.49 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.23 -4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C1 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O11 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.32 -2.43 4.75 2.00e-01 2.50e+01 5.64e+02 ... (remaining 11353 not shown) Planarity restraints: 12180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU u 464 " -0.103 5.00e-02 4.00e+02 1.57e-01 3.96e+01 pdb=" N PRO u 465 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO u 465 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO u 465 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 383 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ARG D 383 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG D 383 " 0.030 2.00e-02 2.50e+03 pdb=" N HIS D 384 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 384 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C HIS D 384 " 0.082 2.00e-02 2.50e+03 pdb=" O HIS D 384 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR D 385 " -0.027 2.00e-02 2.50e+03 ... (remaining 12177 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 1 1.92 - 2.67: 2215 2.67 - 3.41: 98396 3.41 - 4.16: 178030 4.16 - 4.90: 309425 Nonbonded interactions: 588067 Sorted by model distance: nonbonded pdb=" OH TYR A 613 " pdb=" O41 IHP A3001 " model vdw 1.176 3.040 nonbonded pdb=" OP2 G 6 75 " pdb="MG MG 6 202 " model vdw 2.032 2.170 nonbonded pdb=" CZ TYR A 613 " pdb=" O41 IHP A3001 " model vdw 2.033 3.260 nonbonded pdb=" NH2 ARG Q 140 " pdb="ZN ZN Q 202 " model vdw 2.154 2.310 nonbonded pdb=" CE2 TYR A 613 " pdb=" O42 IHP A3001 " model vdw 2.164 3.340 ... (remaining 588062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.020 Check model and map are aligned: 0.400 Set scattering table: 0.510 Process input model: 161.230 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.280 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.011 0.143 74592 Z= 0.693 Angle : 1.315 14.347 102241 Z= 0.714 Chirality : 0.113 4.827 11356 Planarity : 0.009 0.157 12180 Dihedral : 15.314 175.208 29936 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.93 % Favored : 86.77 % Rotamer: Outliers : 1.26 % Allowed : 5.37 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 2.15 % Twisted General : 0.62 % 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: -4.84 (0.07), residues: 8146 helix: -3.20 (0.07), residues: 2798 sheet: -2.34 (0.15), residues: 960 loop : -3.52 (0.08), residues: 4388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 549 HIS 0.027 0.003 HIS B 140 PHE 0.058 0.004 PHE A1192 TYR 0.062 0.005 TYR O 316 ARG 0.032 0.002 ARG A1748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1416 time to evaluate : 5.919 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: 3 612 TYR cc_start: 0.8335 (t80) cc_final: 0.8085 (t80) REVERT: 8 589 ASP cc_start: 0.7595 (t0) cc_final: 0.7378 (t0) REVERT: A 578 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (pp) REVERT: A 599 MET cc_start: 0.8134 (tpp) cc_final: 0.7914 (tpt) REVERT: A 735 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 914 LEU cc_start: 0.8800 (tp) cc_final: 0.8559 (tp) REVERT: A 1370 ARG cc_start: 0.7520 (mmt180) cc_final: 0.6702 (mtp180) REVERT: A 1732 LYS cc_start: 0.8405 (tppt) cc_final: 0.8137 (mmtm) REVERT: A 1781 ASP cc_start: 0.8278 (t0) cc_final: 0.8060 (t0) REVERT: A 1996 ASN cc_start: 0.7568 (t0) cc_final: 0.7302 (t0) REVERT: A 2279 TRP cc_start: 0.6672 (p-90) cc_final: 0.6115 (p-90) REVERT: B 134 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7708 (pp) REVERT: B 236 MET cc_start: 0.6903 (mtm) cc_final: 0.6666 (mtp) REVERT: C 116 TYR cc_start: 0.8319 (t80) cc_final: 0.7852 (t80) REVERT: C 214 ILE cc_start: 0.8791 (mm) cc_final: 0.8449 (mt) REVERT: D 185 MET cc_start: 0.5517 (tmm) cc_final: 0.4794 (tpt) REVERT: D 327 SER cc_start: 0.8246 (m) cc_final: 0.8016 (p) REVERT: D 351 ASP cc_start: 0.7635 (p0) cc_final: 0.7347 (p0) REVERT: E 184 ASN cc_start: 0.7688 (m-40) cc_final: 0.7458 (m-40) REVERT: S 18 TYR cc_start: 0.8201 (t80) cc_final: 0.7955 (t80) REVERT: Y 70 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: u 453 MET cc_start: 0.4322 (mmm) cc_final: 0.4081 (mmt) REVERT: u 953 ASP cc_start: 0.7370 (m-30) cc_final: 0.7125 (m-30) REVERT: u 962 MET cc_start: 0.6776 (mtp) cc_final: 0.6499 (mtt) REVERT: u 1260 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7958 (ptmm) REVERT: v 726 GLN cc_start: 0.7154 (mp10) cc_final: 0.6678 (mp10) REVERT: v 948 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8650 (p) REVERT: x 44 MET cc_start: 0.8326 (ptp) cc_final: 0.8027 (ptm) outliers start: 91 outliers final: 22 residues processed: 1489 average time/residue: 0.8070 time to fit residues: 2014.2165 Evaluate side-chains 905 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 878 time to evaluate : 6.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain z residue 20 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 2.9990 chunk 635 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 428 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 656 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 488 optimal weight: 8.9990 chunk 760 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 5 HIS 8 496 ASN ** 8 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 587 HIS A 439 GLN A 495 GLN A 505 ASN A 563 GLN A 723 ASN A 834 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 924 GLN A1023 ASN A1096 HIS A1293 ASN ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN A1522 GLN A1543 ASN ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 HIS A1998 ASN B 280 HIS B 491 HIS B 583 ASN B 771 GLN B 890 HIS C 106 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS C 283 ASN D 381 HIS ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN O 446 GLN ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 GLN P 120 ASN R 38 HIS R 45 GLN R 196 ASN S 20 GLN ** V 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN s 7 GLN s 88 HIS ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 156 HIS s 169 ASN t 141 GLN t 267 GLN u 459 GLN u 832 GLN ** u 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 912 ASN u1209 ASN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u1277 GLN v 104 GLN ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 526 HIS v 885 ASN ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 55 GLN z 52 ASN z 93 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 74592 Z= 0.388 Angle : 0.856 15.820 102241 Z= 0.443 Chirality : 0.051 0.943 11356 Planarity : 0.007 0.129 12180 Dihedral : 16.446 170.443 13299 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.90 % Favored : 87.99 % Rotamer: Outliers : 3.41 % Allowed : 10.51 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.96 % Twisted General : 0.26 % 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: -3.75 (0.08), residues: 8146 helix: -1.73 (0.09), residues: 2859 sheet: -2.25 (0.15), residues: 999 loop : -3.17 (0.08), residues: 4288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 549 HIS 0.013 0.002 HIS B 140 PHE 0.039 0.002 PHE A1192 TYR 0.036 0.002 TYR A1930 ARG 0.014 0.001 ARG v 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 960 time to evaluate : 5.949 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: A 45 TYR cc_start: 0.5727 (p90) cc_final: 0.5441 (p90) REVERT: A 66 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 642 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8351 (ttt90) REVERT: A 1267 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 1370 ARG cc_start: 0.7450 (mmt180) cc_final: 0.6638 (mtp180) REVERT: A 1405 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6589 (tp) REVERT: A 1513 MET cc_start: 0.6114 (pmm) cc_final: 0.5842 (pmm) REVERT: A 1996 ASN cc_start: 0.7449 (t0) cc_final: 0.7188 (t0) REVERT: B 116 MET cc_start: 0.5708 (mmp) cc_final: 0.4934 (mpp) REVERT: B 134 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7516 (pp) REVERT: B 433 MET cc_start: 0.7007 (ttp) cc_final: 0.6473 (ttm) REVERT: B 465 MET cc_start: 0.7247 (mmm) cc_final: 0.6776 (mmm) REVERT: C 214 ILE cc_start: 0.8809 (mm) cc_final: 0.8538 (mt) REVERT: C 429 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7835 (pt) REVERT: D 185 MET cc_start: 0.5417 (tmm) cc_final: 0.4796 (tpt) REVERT: D 327 SER cc_start: 0.8238 (m) cc_final: 0.7931 (p) REVERT: D 400 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6776 (t80) REVERT: L 37 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8078 (pp) REVERT: O 287 MET cc_start: 0.7989 (ttp) cc_final: 0.7720 (ttp) REVERT: O 319 MET cc_start: 0.8330 (ttp) cc_final: 0.8112 (ttp) REVERT: P 69 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: P 79 ASN cc_start: 0.8176 (t0) cc_final: 0.7905 (t0) REVERT: V 62 ILE cc_start: 0.6268 (mt) cc_final: 0.5959 (mt) REVERT: V 107 THR cc_start: 0.6174 (OUTLIER) cc_final: 0.5680 (p) REVERT: t 141 GLN cc_start: 0.7880 (mt0) cc_final: 0.7619 (mt0) REVERT: t 143 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: t 205 TYR cc_start: 0.8898 (t80) cc_final: 0.8456 (t80) REVERT: u 962 MET cc_start: 0.6461 (mtp) cc_final: 0.6184 (mtt) REVERT: u 1260 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7971 (ptmm) REVERT: v 377 MET cc_start: 0.5668 (ptp) cc_final: 0.5285 (ptp) REVERT: v 948 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8673 (p) REVERT: y 55 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7735 (tp40) REVERT: z 37 ASP cc_start: 0.8111 (t0) cc_final: 0.7699 (t0) REVERT: z 93 ASN cc_start: 0.7229 (m-40) cc_final: 0.7007 (m110) outliers start: 247 outliers final: 127 residues processed: 1147 average time/residue: 0.6901 time to fit residues: 1363.2945 Evaluate side-chains 978 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 839 time to evaluate : 5.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 263 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 136 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 134 THR Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 156 HIS Chi-restraints excluded: chain t residue 143 GLU Chi-restraints excluded: chain u residue 414 VAL Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 828 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1029 GLU Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 55 THR Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 379 LEU Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 689 THR Chi-restraints excluded: chain v residue 728 ARG Chi-restraints excluded: chain v residue 755 VAL Chi-restraints excluded: chain v residue 777 VAL Chi-restraints excluded: chain v residue 865 VAL Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1093 MET Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 633 optimal weight: 0.8980 chunk 518 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 762 optimal weight: 10.0000 chunk 823 optimal weight: 3.9990 chunk 678 optimal weight: 0.0870 chunk 756 optimal weight: 8.9990 chunk 259 optimal weight: 0.6980 chunk 611 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 333 HIS ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN A2084 HIS ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN P 25 GLN P 119 GLN Q 55 GLN V 120 GLN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 127 HIS u 473 GLN u 863 GLN u 891 GLN u 901 GLN u 941 ASN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 304 GLN ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 74592 Z= 0.203 Angle : 0.730 14.731 102241 Z= 0.378 Chirality : 0.046 0.516 11356 Planarity : 0.005 0.114 12180 Dihedral : 16.093 168.524 13292 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.73 % Favored : 89.21 % Rotamer: Outliers : 3.64 % Allowed : 12.15 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -3.10 (0.09), residues: 8146 helix: -0.93 (0.09), residues: 2853 sheet: -1.94 (0.16), residues: 959 loop : -2.97 (0.09), residues: 4334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 313 HIS 0.012 0.001 HIS B 140 PHE 0.032 0.002 PHE A 166 TYR 0.037 0.002 TYR O 416 ARG 0.007 0.001 ARG z 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1001 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 51 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7582 (pp) REVERT: 8 589 ASP cc_start: 0.7593 (t0) cc_final: 0.7377 (t0) REVERT: A 66 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8467 (m) REVERT: A 387 PHE cc_start: 0.6680 (m-10) cc_final: 0.6446 (m-10) REVERT: A 735 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 1359 HIS cc_start: 0.2991 (OUTLIER) cc_final: 0.2650 (t70) REVERT: A 1370 ARG cc_start: 0.7100 (mmt180) cc_final: 0.6518 (mtp180) REVERT: A 1405 LEU cc_start: 0.7061 (mt) cc_final: 0.6830 (tp) REVERT: A 1487 HIS cc_start: 0.6112 (OUTLIER) cc_final: 0.5401 (p90) REVERT: A 1513 MET cc_start: 0.5697 (pmm) cc_final: 0.5491 (pmm) REVERT: A 1960 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (t) REVERT: B 116 MET cc_start: 0.5766 (mmp) cc_final: 0.5311 (mpp) REVERT: B 134 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7476 (pp) REVERT: B 157 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6220 (mp) REVERT: B 203 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6259 (ttm) REVERT: B 433 MET cc_start: 0.6711 (ttp) cc_final: 0.6311 (ttm) REVERT: C 214 ILE cc_start: 0.8711 (mm) cc_final: 0.8476 (mt) REVERT: C 237 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.6020 (ptp) REVERT: C 429 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7732 (pt) REVERT: D 185 MET cc_start: 0.5405 (tmm) cc_final: 0.4900 (tpt) REVERT: D 327 SER cc_start: 0.8131 (m) cc_final: 0.7897 (p) REVERT: D 400 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6579 (t80) REVERT: O 331 GLN cc_start: 0.5535 (tm-30) cc_final: 0.5315 (tm-30) REVERT: V 107 THR cc_start: 0.5959 (OUTLIER) cc_final: 0.5605 (p) REVERT: t 141 GLN cc_start: 0.7930 (mt0) cc_final: 0.7542 (mt0) REVERT: t 205 TYR cc_start: 0.8788 (t80) cc_final: 0.8321 (t80) REVERT: u 703 THR cc_start: 0.9060 (m) cc_final: 0.8830 (p) REVERT: u 839 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7411 (mm-30) REVERT: u 979 TYR cc_start: 0.7931 (t80) cc_final: 0.7698 (t80) REVERT: u 1260 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7954 (ptmm) REVERT: v 131 MET cc_start: 0.8299 (ttm) cc_final: 0.7967 (ttt) REVERT: v 377 MET cc_start: 0.6232 (ptp) cc_final: 0.5692 (ptp) REVERT: v 464 ARG cc_start: 0.4493 (tpt170) cc_final: 0.4147 (tpp80) REVERT: v 948 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8535 (p) REVERT: y 55 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7765 (tp40) REVERT: z 67 ILE cc_start: 0.7182 (mm) cc_final: 0.6897 (mm) outliers start: 264 outliers final: 125 residues processed: 1195 average time/residue: 0.6850 time to fit residues: 1416.1774 Evaluate side-chains 982 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 843 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 891 GLN Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 379 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 689 THR Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 755 VAL Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 9.9990 chunk 573 optimal weight: 3.9990 chunk 395 optimal weight: 0.0670 chunk 84 optimal weight: 0.0670 chunk 363 optimal weight: 4.9990 chunk 511 optimal weight: 3.9990 chunk 765 optimal weight: 0.9980 chunk 810 optimal weight: 0.9980 chunk 399 optimal weight: 0.0870 chunk 725 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 78 HIS A 788 GLN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 GLN A1996 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS C 106 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN D 407 GLN ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN P 119 GLN P 120 ASN V 120 GLN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 891 GLN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 553 GLN ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 HIS y 50 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 74592 Z= 0.182 Angle : 0.700 14.937 102241 Z= 0.359 Chirality : 0.045 0.421 11356 Planarity : 0.005 0.100 12180 Dihedral : 15.862 169.851 13285 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.69 % Favored : 89.25 % Rotamer: Outliers : 3.32 % Allowed : 13.80 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.48 % Twisted General : 0.12 % 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: -2.75 (0.09), residues: 8146 helix: -0.57 (0.10), residues: 2873 sheet: -1.72 (0.16), residues: 944 loop : -2.84 (0.09), residues: 4329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1637 HIS 0.010 0.001 HIS B 140 PHE 0.035 0.001 PHE A 166 TYR 0.028 0.001 TYR B 66 ARG 0.011 0.000 ARG z 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 928 time to evaluate : 5.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 509 GLN cc_start: 0.7125 (pp30) cc_final: 0.6867 (pp30) REVERT: A 66 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 316 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7357 (p90) REVERT: A 387 PHE cc_start: 0.6621 (m-10) cc_final: 0.6315 (m-10) REVERT: A 735 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 1370 ARG cc_start: 0.7024 (mmt180) cc_final: 0.6519 (mtp180) REVERT: A 1487 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5407 (p90) REVERT: A 1732 LYS cc_start: 0.8454 (tppt) cc_final: 0.8229 (mmtm) REVERT: A 1745 GLU cc_start: 0.7383 (pp20) cc_final: 0.7131 (pp20) REVERT: A 1960 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8803 (t) REVERT: A 2090 ILE cc_start: 0.6098 (OUTLIER) cc_final: 0.5222 (tp) REVERT: A 2200 MET cc_start: 0.4988 (OUTLIER) cc_final: 0.4319 (tpp) REVERT: A 2270 PHE cc_start: 0.6141 (p90) cc_final: 0.5812 (p90) REVERT: B 116 MET cc_start: 0.5824 (mmp) cc_final: 0.5363 (mpp) REVERT: B 134 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7484 (pp) REVERT: B 157 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.5867 (mm) REVERT: B 433 MET cc_start: 0.6712 (ttp) cc_final: 0.6302 (ttm) REVERT: B 939 ARG cc_start: 0.6268 (ttt180) cc_final: 0.5639 (ttm-80) REVERT: C 214 ILE cc_start: 0.8683 (mm) cc_final: 0.8437 (mt) REVERT: C 429 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7723 (pt) REVERT: D 185 MET cc_start: 0.5215 (tmm) cc_final: 0.4798 (tpt) REVERT: D 327 SER cc_start: 0.8104 (m) cc_final: 0.7882 (p) REVERT: L 37 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8035 (pp) REVERT: L 69 GLU cc_start: 0.6536 (pp20) cc_final: 0.6250 (pp20) REVERT: O 411 MET cc_start: 0.3604 (tmm) cc_final: 0.3327 (tmm) REVERT: O 453 LYS cc_start: 0.4821 (ptpp) cc_final: 0.4314 (tttt) REVERT: R 30 TYR cc_start: 0.6928 (m-80) cc_final: 0.6328 (m-80) REVERT: R 72 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6443 (ppp-140) REVERT: V 107 THR cc_start: 0.6087 (OUTLIER) cc_final: 0.5786 (p) REVERT: Y 70 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7847 (t80) REVERT: t 141 GLN cc_start: 0.7883 (mt0) cc_final: 0.7519 (mt0) REVERT: t 205 TYR cc_start: 0.8757 (t80) cc_final: 0.8265 (t80) REVERT: u 495 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6243 (ppt170) REVERT: u 703 THR cc_start: 0.9036 (m) cc_final: 0.8786 (p) REVERT: u 1260 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7979 (ptmm) REVERT: v 131 MET cc_start: 0.8301 (ttm) cc_final: 0.7943 (ttt) REVERT: v 948 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8445 (p) outliers start: 241 outliers final: 151 residues processed: 1107 average time/residue: 0.6939 time to fit residues: 1328.4055 Evaluate side-chains 996 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 829 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 156 HIS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 495 ARG Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 727 VAL Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 0.5980 chunk 459 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 603 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 691 optimal weight: 0.0020 chunk 559 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.4980 chunk 727 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 506 GLN 3 508 GLN A 723 ASN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN ** A2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 ASN ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 GLN P 251 HIS Y 97 ASN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 891 GLN u 973 HIS ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 58 ASN y 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 74592 Z= 0.178 Angle : 0.688 14.779 102241 Z= 0.351 Chirality : 0.044 0.409 11356 Planarity : 0.005 0.089 12180 Dihedral : 15.666 171.517 13281 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.55 % Favored : 89.41 % Rotamer: Outliers : 3.74 % Allowed : 14.42 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.48 % Twisted General : 0.13 % 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: -2.47 (0.09), residues: 8146 helix: -0.26 (0.10), residues: 2876 sheet: -1.59 (0.16), residues: 954 loop : -2.73 (0.09), residues: 4316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP O 336 HIS 0.010 0.001 HIS B 140 PHE 0.035 0.001 PHE A 166 TYR 0.025 0.001 TYR B 66 ARG 0.011 0.000 ARG A1748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 939 time to evaluate : 6.009 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: 1 61 GLU cc_start: 0.5202 (tp30) cc_final: 0.4950 (tp30) REVERT: 3 509 GLN cc_start: 0.7016 (pp30) cc_final: 0.6580 (pp30) REVERT: 7 21 GLU cc_start: 0.7207 (tt0) cc_final: 0.6592 (tt0) REVERT: 7 51 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7526 (pp) REVERT: A 45 TYR cc_start: 0.5732 (p90) cc_final: 0.5516 (p90) REVERT: A 66 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8497 (m) REVERT: A 735 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 1370 ARG cc_start: 0.7023 (mmt180) cc_final: 0.6366 (mtm180) REVERT: A 1487 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5588 (p90) REVERT: A 1930 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: A 1967 ILE cc_start: 0.8307 (pp) cc_final: 0.7747 (pt) REVERT: A 2200 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4591 (tpp) REVERT: B 116 MET cc_start: 0.5735 (mmp) cc_final: 0.5167 (mpp) REVERT: B 134 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7364 (pp) REVERT: B 433 MET cc_start: 0.6848 (ttp) cc_final: 0.6329 (ttm) REVERT: B 939 ARG cc_start: 0.6368 (ttt180) cc_final: 0.5761 (ttm-80) REVERT: C 214 ILE cc_start: 0.8635 (mm) cc_final: 0.8413 (mt) REVERT: C 429 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7634 (pt) REVERT: D 185 MET cc_start: 0.5342 (tmm) cc_final: 0.4886 (tpt) REVERT: D 474 GLU cc_start: 0.7246 (mp0) cc_final: 0.7004 (mp0) REVERT: L 37 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8044 (pp) REVERT: L 69 GLU cc_start: 0.6573 (pp20) cc_final: 0.6304 (pp20) REVERT: O 404 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.5735 (pm20) REVERT: O 453 LYS cc_start: 0.4982 (ptpp) cc_final: 0.4411 (tttt) REVERT: P 208 PRO cc_start: 0.6005 (Cg_endo) cc_final: 0.5592 (Cg_exo) REVERT: R 72 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6343 (ppp-140) REVERT: V 161 LYS cc_start: 0.6278 (tmtt) cc_final: 0.5495 (tttp) REVERT: Y 70 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.8010 (t80) REVERT: Y 90 THR cc_start: 0.8240 (p) cc_final: 0.8020 (p) REVERT: Y 96 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7112 (ttmm) REVERT: t 141 GLN cc_start: 0.7817 (mt0) cc_final: 0.7510 (mt0) REVERT: t 205 TYR cc_start: 0.8741 (t80) cc_final: 0.8235 (t80) REVERT: u 477 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7792 (mtmm) REVERT: u 703 THR cc_start: 0.9025 (m) cc_final: 0.8756 (p) REVERT: u 769 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8276 (p) REVERT: u 979 TYR cc_start: 0.8071 (t80) cc_final: 0.7870 (t80) REVERT: u 1154 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8853 (tt) REVERT: u 1260 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7999 (ptmm) REVERT: v 131 MET cc_start: 0.8217 (ttm) cc_final: 0.7862 (ttt) REVERT: v 339 MET cc_start: 0.7555 (ptp) cc_final: 0.7348 (ptm) REVERT: v 478 PHE cc_start: 0.5752 (p90) cc_final: 0.5548 (p90) REVERT: v 736 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6667 (t80) REVERT: v 948 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8439 (p) REVERT: y 50 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7250 (t0) REVERT: z 47 GLN cc_start: 0.6125 (pt0) cc_final: 0.5859 (pt0) outliers start: 271 outliers final: 160 residues processed: 1142 average time/residue: 0.6897 time to fit residues: 1362.3006 Evaluate side-chains 1010 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 831 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain V residue 15 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain Y residue 96 LYS Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 414 VAL Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 769 VAL Chi-restraints excluded: chain u residue 773 LEU Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1154 LEU Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 6.9990 chunk 729 optimal weight: 0.8980 chunk 160 optimal weight: 0.0970 chunk 475 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 810 optimal weight: 1.9990 chunk 673 optimal weight: 0.7980 chunk 375 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 425 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 506 GLN 3 508 GLN A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 GLN A1996 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 924 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 324 HIS ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 HIS ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 985 HIS ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 74592 Z= 0.233 Angle : 0.697 14.895 102241 Z= 0.355 Chirality : 0.045 0.584 11356 Planarity : 0.005 0.081 12180 Dihedral : 15.596 171.774 13280 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.70 % Favored : 89.25 % Rotamer: Outliers : 3.68 % Allowed : 15.23 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.48 % Twisted General : 0.10 % 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: -2.34 (0.09), residues: 8146 helix: -0.13 (0.10), residues: 2873 sheet: -1.47 (0.17), residues: 944 loop : -2.68 (0.09), residues: 4329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1637 HIS 0.018 0.001 HIS P 251 PHE 0.041 0.001 PHE A 166 TYR 0.024 0.002 TYR t 297 ARG 0.009 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 868 time to evaluate : 6.165 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: 1 61 GLU cc_start: 0.5369 (tp30) cc_final: 0.4993 (tp30) REVERT: 3 509 GLN cc_start: 0.7111 (pp30) cc_final: 0.6678 (pp30) REVERT: 7 21 GLU cc_start: 0.7404 (tt0) cc_final: 0.7061 (tt0) REVERT: 7 51 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7631 (pp) REVERT: 8 553 MET cc_start: 0.8468 (mmm) cc_final: 0.8106 (mmm) REVERT: A 45 TYR cc_start: 0.5815 (p90) cc_final: 0.5529 (p90) REVERT: A 735 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 834 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6754 (m-70) REVERT: A 1370 ARG cc_start: 0.7091 (mmt180) cc_final: 0.6484 (mtm180) REVERT: A 1487 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5988 (p90) REVERT: A 1745 GLU cc_start: 0.7494 (pp20) cc_final: 0.7193 (pp20) REVERT: A 1930 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: A 2012 LEU cc_start: 0.8713 (pp) cc_final: 0.8150 (pp) REVERT: A 2200 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4693 (tpp) REVERT: B 116 MET cc_start: 0.5945 (mmp) cc_final: 0.5382 (mpp) REVERT: B 134 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7281 (pp) REVERT: B 433 MET cc_start: 0.6905 (ttp) cc_final: 0.6298 (ttm) REVERT: B 668 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: C 129 ASP cc_start: 0.5461 (p0) cc_final: 0.5229 (p0) REVERT: C 214 ILE cc_start: 0.8721 (mm) cc_final: 0.8470 (mt) REVERT: C 429 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7807 (pt) REVERT: D 185 MET cc_start: 0.5258 (tmm) cc_final: 0.4854 (tpt) REVERT: D 474 GLU cc_start: 0.7273 (mp0) cc_final: 0.7040 (mp0) REVERT: L 37 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8092 (pp) REVERT: O 404 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5707 (pm20) REVERT: P 208 PRO cc_start: 0.6055 (Cg_endo) cc_final: 0.5641 (Cg_exo) REVERT: P 251 HIS cc_start: 0.2979 (OUTLIER) cc_final: 0.2572 (t-90) REVERT: R 30 TYR cc_start: 0.6752 (m-80) cc_final: 0.6273 (m-80) REVERT: R 72 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6406 (ppp-140) REVERT: V 107 THR cc_start: 0.6045 (OUTLIER) cc_final: 0.5445 (p) REVERT: V 161 LYS cc_start: 0.6196 (tmtt) cc_final: 0.5421 (tttp) REVERT: Y 40 MET cc_start: 0.7104 (mmm) cc_final: 0.6669 (mmp) REVERT: Y 70 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8051 (t80) REVERT: Y 90 THR cc_start: 0.8311 (p) cc_final: 0.8088 (p) REVERT: t 141 GLN cc_start: 0.7770 (mt0) cc_final: 0.7452 (mt0) REVERT: t 205 TYR cc_start: 0.8791 (t80) cc_final: 0.8292 (t80) REVERT: u 477 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7724 (mtmm) REVERT: u 540 MET cc_start: 0.6554 (tpt) cc_final: 0.6004 (tpt) REVERT: u 703 THR cc_start: 0.9027 (m) cc_final: 0.8765 (p) REVERT: u 1178 MET cc_start: 0.7478 (mtm) cc_final: 0.7170 (mtm) REVERT: u 1260 LYS cc_start: 0.8230 (ttpp) cc_final: 0.8006 (ptmm) REVERT: v 131 MET cc_start: 0.8295 (ttm) cc_final: 0.7935 (ttt) REVERT: v 478 PHE cc_start: 0.5879 (p90) cc_final: 0.5659 (p90) REVERT: v 736 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6902 (t80) REVERT: v 948 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8475 (p) REVERT: y 50 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7071 (t0) REVERT: z 46 ARG cc_start: 0.6323 (mmm160) cc_final: 0.6040 (mmm-85) outliers start: 267 outliers final: 187 residues processed: 1072 average time/residue: 0.6763 time to fit residues: 1258.1769 Evaluate side-chains 1016 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 810 time to evaluate : 5.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 692 HIS Chi-restraints excluded: chain u residue 727 VAL Chi-restraints excluded: chain u residue 773 LEU Chi-restraints excluded: chain u residue 784 MET Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 914 ILE Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 23 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 461 optimal weight: 1.9990 chunk 592 optimal weight: 6.9990 chunk 458 optimal weight: 0.9990 chunk 682 optimal weight: 4.9990 chunk 452 optimal weight: 7.9990 chunk 807 optimal weight: 0.9980 chunk 505 optimal weight: 0.9990 chunk 492 optimal weight: 0.9980 chunk 372 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 506 GLN A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN ** A2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 HIS Q 95 GLN s 42 GLN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 74592 Z= 0.234 Angle : 0.701 14.927 102241 Z= 0.357 Chirality : 0.045 0.533 11356 Planarity : 0.005 0.076 12180 Dihedral : 15.558 171.782 13280 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.94 % Favored : 89.01 % Rotamer: Outliers : 3.85 % Allowed : 15.53 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.24 % Twisted General : 0.10 % 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: -2.26 (0.09), residues: 8146 helix: -0.03 (0.10), residues: 2861 sheet: -1.60 (0.16), residues: 970 loop : -2.61 (0.09), residues: 4315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 63 HIS 0.010 0.001 HIS P 251 PHE 0.037 0.001 PHE A 166 TYR 0.023 0.002 TYR B 817 ARG 0.009 0.000 ARG z 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 864 time to evaluate : 5.894 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: 3 509 GLN cc_start: 0.7168 (pp30) cc_final: 0.6736 (pp30) REVERT: 7 21 GLU cc_start: 0.7298 (tt0) cc_final: 0.7021 (tt0) REVERT: 7 51 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7632 (pp) REVERT: 8 549 MET cc_start: 0.8077 (tpp) cc_final: 0.7583 (ttm) REVERT: 8 553 MET cc_start: 0.8523 (mmm) cc_final: 0.8114 (mmm) REVERT: A 45 TYR cc_start: 0.5925 (p90) cc_final: 0.5686 (p90) REVERT: A 316 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6749 (p90) REVERT: A 735 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 834 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6767 (m-70) REVERT: A 1311 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: A 1370 ARG cc_start: 0.7298 (mmt180) cc_final: 0.6669 (mtm180) REVERT: A 1467 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8854 (pp) REVERT: A 1930 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: A 2090 ILE cc_start: 0.6036 (OUTLIER) cc_final: 0.5236 (tp) REVERT: A 2103 THR cc_start: 0.5142 (OUTLIER) cc_final: 0.4804 (t) REVERT: A 2200 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4712 (tpp) REVERT: B 116 MET cc_start: 0.6225 (mmp) cc_final: 0.5614 (mpp) REVERT: B 134 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7347 (pp) REVERT: B 433 MET cc_start: 0.6943 (ttp) cc_final: 0.6316 (ttm) REVERT: B 652 ASP cc_start: 0.7588 (p0) cc_final: 0.7381 (p0) REVERT: B 668 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: C 214 ILE cc_start: 0.8734 (mm) cc_final: 0.8477 (mt) REVERT: C 429 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7885 (pt) REVERT: D 185 MET cc_start: 0.5160 (tmm) cc_final: 0.4640 (tpt) REVERT: L 37 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8091 (pp) REVERT: O 404 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.5783 (pm20) REVERT: P 208 PRO cc_start: 0.6123 (Cg_endo) cc_final: 0.5726 (Cg_exo) REVERT: P 251 HIS cc_start: 0.2812 (OUTLIER) cc_final: 0.1205 (t-90) REVERT: R 72 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6381 (ppp-140) REVERT: V 107 THR cc_start: 0.5893 (OUTLIER) cc_final: 0.5260 (p) REVERT: V 161 LYS cc_start: 0.6141 (tmtt) cc_final: 0.5340 (tttp) REVERT: Y 70 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8043 (t80) REVERT: Y 90 THR cc_start: 0.8245 (p) cc_final: 0.8041 (p) REVERT: s 174 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6249 (tt) REVERT: t 141 GLN cc_start: 0.7800 (mt0) cc_final: 0.7455 (mt0) REVERT: t 205 TYR cc_start: 0.8812 (t80) cc_final: 0.8344 (t80) REVERT: u 477 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7635 (mtmm) REVERT: u 540 MET cc_start: 0.6588 (tpt) cc_final: 0.6072 (tpt) REVERT: u 703 THR cc_start: 0.9035 (m) cc_final: 0.8771 (p) REVERT: u 981 TYR cc_start: 0.7797 (m-80) cc_final: 0.7543 (m-80) REVERT: u 1178 MET cc_start: 0.7571 (mtm) cc_final: 0.7257 (mtm) REVERT: u 1260 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7986 (ptmm) REVERT: v 131 MET cc_start: 0.8335 (ttm) cc_final: 0.7949 (ttt) REVERT: v 478 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5706 (p90) REVERT: v 736 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7116 (t80) REVERT: v 948 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8477 (p) REVERT: x 48 ASP cc_start: 0.6302 (t70) cc_final: 0.5905 (t0) outliers start: 279 outliers final: 203 residues processed: 1070 average time/residue: 0.6883 time to fit residues: 1283.2024 Evaluate side-chains 1045 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 818 time to evaluate : 5.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 389 HIS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 15 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 112 GLU Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 153 TYR Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 656 LYS Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 692 HIS Chi-restraints excluded: chain u residue 727 VAL Chi-restraints excluded: chain u residue 784 MET Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 23 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 482 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 513 optimal weight: 6.9990 chunk 550 optimal weight: 2.9990 chunk 399 optimal weight: 0.0570 chunk 75 optimal weight: 0.5980 chunk 634 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 HIS Q 55 GLN ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 74592 Z= 0.184 Angle : 0.687 15.011 102241 Z= 0.348 Chirality : 0.044 0.440 11356 Planarity : 0.005 0.068 12180 Dihedral : 15.483 172.270 13278 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.45 % Favored : 89.53 % Rotamer: Outliers : 3.46 % Allowed : 16.39 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.24 % Twisted General : 0.10 % 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: -2.14 (0.09), residues: 8146 helix: 0.08 (0.10), residues: 2871 sheet: -1.45 (0.16), residues: 940 loop : -2.57 (0.09), residues: 4335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1637 HIS 0.016 0.001 HIS P 251 PHE 0.035 0.001 PHE A 166 TYR 0.030 0.001 TYR B 65 ARG 0.008 0.000 ARG 3 505 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 898 time to evaluate : 5.985 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: 3 509 GLN cc_start: 0.7172 (pp30) cc_final: 0.6774 (pp30) REVERT: 7 51 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7747 (pp) REVERT: A 45 TYR cc_start: 0.5740 (p90) cc_final: 0.5516 (p90) REVERT: A 316 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7183 (p90) REVERT: A 320 TYR cc_start: 0.6925 (m-80) cc_final: 0.6719 (m-80) REVERT: A 735 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 1094 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7462 (mmt-90) REVERT: A 1123 GLU cc_start: 0.6071 (mp0) cc_final: 0.5649 (mp0) REVERT: A 1311 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: A 1370 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6725 (mtp180) REVERT: A 1467 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (pp) REVERT: A 1930 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: A 2090 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5228 (tp) REVERT: A 2103 THR cc_start: 0.5099 (OUTLIER) cc_final: 0.4811 (t) REVERT: A 2200 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4874 (tpp) REVERT: B 116 MET cc_start: 0.6200 (mmp) cc_final: 0.5584 (mpp) REVERT: B 134 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7392 (pp) REVERT: B 186 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 433 MET cc_start: 0.6868 (ttp) cc_final: 0.6294 (ttm) REVERT: B 668 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: C 138 GLU cc_start: 0.7911 (mp0) cc_final: 0.7561 (mp0) REVERT: C 214 ILE cc_start: 0.8609 (mm) cc_final: 0.8344 (mt) REVERT: C 429 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7889 (pt) REVERT: D 185 MET cc_start: 0.5018 (tmm) cc_final: 0.4484 (tpt) REVERT: D 474 GLU cc_start: 0.7304 (mp0) cc_final: 0.6961 (mp0) REVERT: L 37 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8022 (pp) REVERT: L 62 GLU cc_start: 0.8264 (pm20) cc_final: 0.7969 (pm20) REVERT: L 66 GLU cc_start: 0.6242 (mp0) cc_final: 0.5764 (mp0) REVERT: O 404 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5699 (pm20) REVERT: O 411 MET cc_start: 0.2769 (tmm) cc_final: 0.1863 (tmm) REVERT: P 208 PRO cc_start: 0.6151 (Cg_endo) cc_final: 0.5734 (Cg_exo) REVERT: R 72 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6352 (ppp-140) REVERT: V 107 THR cc_start: 0.5661 (OUTLIER) cc_final: 0.5105 (p) REVERT: V 161 LYS cc_start: 0.5955 (tmtt) cc_final: 0.5129 (tttp) REVERT: Y 70 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8040 (t80) REVERT: Y 90 THR cc_start: 0.8163 (p) cc_final: 0.7955 (p) REVERT: s 174 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6209 (tt) REVERT: t 141 GLN cc_start: 0.7647 (mt0) cc_final: 0.7258 (mt0) REVERT: t 205 TYR cc_start: 0.8790 (t80) cc_final: 0.8287 (t80) REVERT: u 451 ARG cc_start: 0.7204 (ptp-170) cc_final: 0.6883 (mmm160) REVERT: u 477 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7516 (mtmm) REVERT: u 540 MET cc_start: 0.6516 (tpt) cc_final: 0.6006 (tpt) REVERT: u 703 THR cc_start: 0.9014 (m) cc_final: 0.8759 (p) REVERT: u 981 TYR cc_start: 0.7658 (m-80) cc_final: 0.7216 (m-80) REVERT: u 1133 MET cc_start: 0.8673 (mtp) cc_final: 0.8442 (mtp) REVERT: u 1154 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8838 (tt) REVERT: u 1178 MET cc_start: 0.7539 (mtm) cc_final: 0.7225 (mtm) REVERT: u 1260 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7987 (ptmm) REVERT: v 131 MET cc_start: 0.8237 (ttm) cc_final: 0.7887 (ttt) REVERT: v 478 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.5714 (p90) REVERT: v 736 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.7151 (t80) REVERT: v 948 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8431 (p) REVERT: y 55 GLN cc_start: 0.7379 (tp40) cc_final: 0.7149 (tp-100) outliers start: 251 outliers final: 180 residues processed: 1080 average time/residue: 0.7113 time to fit residues: 1331.4797 Evaluate side-chains 1035 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 831 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 389 HIS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain V residue 15 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 112 GLU Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 153 TYR Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 692 HIS Chi-restraints excluded: chain u residue 784 MET Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1021 THR Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1154 LEU Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 27 THR Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 23 ILE Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 5.9990 chunk 773 optimal weight: 4.9990 chunk 705 optimal weight: 0.9980 chunk 752 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 591 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 680 optimal weight: 0.8980 chunk 711 optimal weight: 0.6980 chunk 750 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 506 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 GLN A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1784 ASN A1894 GLN A1996 ASN ** A2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 GLN Q 55 GLN ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 74592 Z= 0.225 Angle : 0.696 15.044 102241 Z= 0.354 Chirality : 0.045 0.660 11356 Planarity : 0.005 0.082 12180 Dihedral : 15.455 172.253 13278 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.80 % Favored : 89.17 % Rotamer: Outliers : 3.35 % Allowed : 16.73 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.24 % Twisted General : 0.10 % 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: -2.10 (0.09), residues: 8146 helix: 0.08 (0.10), residues: 2885 sheet: -1.46 (0.17), residues: 937 loop : -2.53 (0.09), residues: 4324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP O 336 HIS 0.036 0.001 HIS A1487 PHE 0.035 0.001 PHE A 166 TYR 0.027 0.001 TYR x 43 ARG 0.015 0.000 ARG 3 505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 852 time to evaluate : 5.935 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: 3 509 GLN cc_start: 0.7229 (pp30) cc_final: 0.6859 (pp30) REVERT: 7 51 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7827 (pp) REVERT: A 45 TYR cc_start: 0.5770 (p90) cc_final: 0.5539 (p90) REVERT: A 316 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6897 (p90) REVERT: A 320 TYR cc_start: 0.6906 (m-80) cc_final: 0.6637 (m-80) REVERT: A 735 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8227 (mt) REVERT: A 834 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6791 (m-70) REVERT: A 1094 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7429 (mmt-90) REVERT: A 1123 GLU cc_start: 0.5802 (mp0) cc_final: 0.5441 (mp0) REVERT: A 1311 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 1370 ARG cc_start: 0.7288 (mmt180) cc_final: 0.6642 (mtm180) REVERT: A 1467 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8844 (pp) REVERT: A 1930 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: A 2090 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5238 (tp) REVERT: A 2103 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4887 (t) REVERT: A 2200 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.4930 (tpp) REVERT: B 116 MET cc_start: 0.6210 (mmp) cc_final: 0.5561 (mpp) REVERT: B 134 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7310 (pp) REVERT: B 186 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7835 (m) REVERT: B 203 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6363 (ttm) REVERT: B 433 MET cc_start: 0.7001 (ttp) cc_final: 0.6384 (ttm) REVERT: B 668 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: C 129 ASP cc_start: 0.4836 (m-30) cc_final: 0.4509 (p0) REVERT: C 138 GLU cc_start: 0.7976 (mp0) cc_final: 0.7629 (mp0) REVERT: C 214 ILE cc_start: 0.8819 (mm) cc_final: 0.8568 (mt) REVERT: C 427 ASP cc_start: 0.8221 (p0) cc_final: 0.7957 (p0) REVERT: C 429 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7959 (pt) REVERT: D 185 MET cc_start: 0.4996 (tmm) cc_final: 0.4470 (tpt) REVERT: D 474 GLU cc_start: 0.7393 (mp0) cc_final: 0.7072 (mp0) REVERT: L 37 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8036 (pp) REVERT: L 62 GLU cc_start: 0.8279 (pm20) cc_final: 0.7996 (pm20) REVERT: O 404 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5647 (pm20) REVERT: O 411 MET cc_start: 0.3335 (tmm) cc_final: 0.2281 (tmm) REVERT: P 208 PRO cc_start: 0.6207 (Cg_endo) cc_final: 0.5806 (Cg_exo) REVERT: R 72 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6306 (ppp-140) REVERT: V 107 THR cc_start: 0.5239 (OUTLIER) cc_final: 0.4668 (p) REVERT: V 161 LYS cc_start: 0.5914 (tmtt) cc_final: 0.5083 (tttp) REVERT: Y 90 THR cc_start: 0.8141 (p) cc_final: 0.7892 (p) REVERT: s 174 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6124 (tt) REVERT: t 141 GLN cc_start: 0.7630 (mt0) cc_final: 0.7252 (mt0) REVERT: t 205 TYR cc_start: 0.8805 (t80) cc_final: 0.8304 (t80) REVERT: u 477 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7506 (mtmm) REVERT: u 540 MET cc_start: 0.6544 (tpt) cc_final: 0.6035 (tpt) REVERT: u 703 THR cc_start: 0.9022 (m) cc_final: 0.8767 (p) REVERT: u 1178 MET cc_start: 0.7598 (mtm) cc_final: 0.7305 (mtm) REVERT: u 1260 LYS cc_start: 0.8258 (ttpp) cc_final: 0.8005 (ptmm) REVERT: v 131 MET cc_start: 0.8326 (ttm) cc_final: 0.7959 (ttt) REVERT: v 478 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.5781 (p90) REVERT: v 736 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7212 (t80) REVERT: v 948 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8452 (p) REVERT: x 48 ASP cc_start: 0.6166 (t70) cc_final: 0.5702 (t0) REVERT: y 55 GLN cc_start: 0.7428 (tp40) cc_final: 0.7067 (tp40) outliers start: 243 outliers final: 185 residues processed: 1028 average time/residue: 0.6754 time to fit residues: 1210.3741 Evaluate side-chains 1023 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 814 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 VAL Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 250 GLN Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 389 HIS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 15 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 112 GLU Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 153 TYR Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 692 HIS Chi-restraints excluded: chain u residue 727 VAL Chi-restraints excluded: chain u residue 784 MET Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1021 THR Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 27 THR Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 23 ILE Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 0.0570 chunk 795 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 553 optimal weight: 3.9990 chunk 834 optimal weight: 0.7980 chunk 768 optimal weight: 0.9980 chunk 664 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 513 optimal weight: 0.2980 chunk 407 optimal weight: 0.0370 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 473 GLN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v1052 ASN y 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 74592 Z= 0.174 Angle : 0.685 15.105 102241 Z= 0.347 Chirality : 0.044 0.611 11356 Planarity : 0.005 0.066 12180 Dihedral : 15.373 172.854 13276 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.14 % Favored : 89.85 % Rotamer: Outliers : 2.95 % Allowed : 17.26 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.00 (0.09), residues: 8146 helix: 0.20 (0.10), residues: 2869 sheet: -1.32 (0.17), residues: 913 loop : -2.49 (0.09), residues: 4364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP O 336 HIS 0.031 0.001 HIS A1487 PHE 0.036 0.001 PHE A 166 TYR 0.030 0.001 TYR x 43 ARG 0.024 0.000 ARG z 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 897 time to evaluate : 6.066 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: 7 51 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7748 (pp) REVERT: A 316 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6956 (p90) REVERT: A 320 TYR cc_start: 0.6799 (m-80) cc_final: 0.6556 (m-80) REVERT: A 423 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5946 (m-30) REVERT: A 735 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 1311 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: A 1370 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6645 (mtm180) REVERT: A 1467 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8759 (pp) REVERT: A 1706 ASP cc_start: 0.7792 (t0) cc_final: 0.7515 (t0) REVERT: A 1930 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: A 2090 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5372 (tp) REVERT: A 2103 THR cc_start: 0.4968 (OUTLIER) cc_final: 0.4716 (t) REVERT: A 2200 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4830 (tpp) REVERT: B 116 MET cc_start: 0.6088 (mmp) cc_final: 0.5482 (mpp) REVERT: B 134 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7400 (pp) REVERT: B 186 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7822 (m) REVERT: B 261 ASP cc_start: 0.6817 (p0) cc_final: 0.6563 (p0) REVERT: B 327 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.6573 (t80) REVERT: B 433 MET cc_start: 0.6926 (ttp) cc_final: 0.6312 (ttm) REVERT: C 129 ASP cc_start: 0.4750 (m-30) cc_final: 0.4447 (p0) REVERT: C 138 GLU cc_start: 0.7936 (mp0) cc_final: 0.7660 (mp0) REVERT: C 214 ILE cc_start: 0.8511 (mm) cc_final: 0.8258 (mt) REVERT: C 429 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7836 (pt) REVERT: D 185 MET cc_start: 0.4910 (tmm) cc_final: 0.4400 (tpt) REVERT: D 474 GLU cc_start: 0.7393 (mp0) cc_final: 0.7059 (mp0) REVERT: L 37 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7952 (pp) REVERT: O 404 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5619 (pm20) REVERT: O 411 MET cc_start: 0.3092 (tmm) cc_final: 0.2161 (tmm) REVERT: P 208 PRO cc_start: 0.6216 (Cg_endo) cc_final: 0.5800 (Cg_exo) REVERT: Q 29 MET cc_start: 0.8631 (tpt) cc_final: 0.8359 (tpt) REVERT: R 72 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6304 (ppp-140) REVERT: V 98 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7004 (mt) REVERT: V 159 ILE cc_start: 0.4601 (mt) cc_final: 0.4200 (mm) REVERT: V 161 LYS cc_start: 0.5904 (tmtt) cc_final: 0.5133 (tttp) REVERT: Y 79 ASN cc_start: 0.6509 (m110) cc_final: 0.6296 (m-40) REVERT: Y 90 THR cc_start: 0.8122 (p) cc_final: 0.7876 (p) REVERT: t 141 GLN cc_start: 0.7644 (mt0) cc_final: 0.7258 (mt0) REVERT: t 205 TYR cc_start: 0.8770 (t80) cc_final: 0.8272 (t80) REVERT: u 477 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7334 (mtmm) REVERT: u 540 MET cc_start: 0.6505 (tpt) cc_final: 0.5998 (tpt) REVERT: u 703 THR cc_start: 0.8962 (m) cc_final: 0.8710 (p) REVERT: u 1178 MET cc_start: 0.7533 (mtm) cc_final: 0.7248 (mtm) REVERT: u 1260 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7976 (ptmm) REVERT: v 131 MET cc_start: 0.8213 (ttm) cc_final: 0.7935 (ttt) REVERT: v 377 MET cc_start: 0.6173 (pmm) cc_final: 0.5790 (pmm) REVERT: v 478 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.5810 (p90) REVERT: v 736 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7210 (t80) REVERT: v 948 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8403 (p) outliers start: 214 outliers final: 163 residues processed: 1042 average time/residue: 0.7076 time to fit residues: 1288.4141 Evaluate side-chains 1015 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 830 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1359 HIS Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 250 GLN Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 389 HIS Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain V residue 15 TYR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 153 TYR Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 691 GLU Chi-restraints excluded: chain u residue 692 HIS Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1021 THR Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 726 GLN Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 23 ILE Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 3.9990 chunk 708 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 612 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 665 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 683 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 78 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN A1996 ASN ** A2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u1091 HIS ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.101261 restraints weight = 151855.740| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.18 r_work: 0.3304 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 74592 Z= 0.209 Angle : 0.696 15.157 102241 Z= 0.353 Chirality : 0.045 0.598 11356 Planarity : 0.005 0.067 12180 Dihedral : 15.354 172.841 13275 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.77 % Favored : 89.22 % Rotamer: Outliers : 2.95 % Allowed : 17.60 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.96 (0.09), residues: 8146 helix: 0.23 (0.10), residues: 2879 sheet: -1.30 (0.17), residues: 891 loop : -2.47 (0.09), residues: 4376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP O 336 HIS 0.031 0.001 HIS A1487 PHE 0.035 0.001 PHE A 166 TYR 0.028 0.001 TYR A1369 ARG 0.014 0.000 ARG z 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21865.75 seconds wall clock time: 377 minutes 41.63 seconds (22661.63 seconds total)