Starting phenix.real_space_refine on Mon Mar 25 10:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/03_2024/5iyc_8137.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 11 6.06 5 P 158 5.49 5 Mg 2 5.21 5 S 270 5.16 5 C 29697 2.51 5 N 8418 2.21 5 O 9371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 897": "NH1" <-> "NH2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M ARG 248": "NH1" <-> "NH2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "N ASP 340": "OD1" <-> "OD2" Residue "N ARG 363": "NH1" <-> "NH2" Residue "O GLU 21": "OE1" <-> "OE2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P GLU 206": "OE1" <-> "OE2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 269": "NH1" <-> "NH2" Residue "P ARG 294": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q ARG 179": "NH1" <-> "NH2" Residue "Q ARG 192": "NH1" <-> "NH2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R ASP 213": "OD1" <-> "OD2" Residue "R GLU 230": "OE1" <-> "OE2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T GLU 133": "OE1" <-> "OE2" Residue "U ARG 192": "NH1" <-> "NH2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47927 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1454, 11515 Classifications: {'peptide': 1454} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1384} Chain breaks: 1 Chain: "B" Number of atoms: 9317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9317 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 53, 'TRANS': 1111} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2213 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1062 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1205 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1013 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2391 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "P" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1484 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "U" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1343 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "X" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1645 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Y" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1624 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 52.496 116.861 106.459 1.00 0.00 S ATOM 494 SG CYS A 74 51.834 120.887 107.486 1.00 0.00 S ATOM 541 SG CYS A 81 53.736 118.771 104.063 1.00 0.00 S ATOM 776 SG CYS A 111 100.613 118.808 114.297 1.00 0.00 S ATOM 804 SG CYS A 114 100.325 120.420 118.319 1.00 0.00 S ATOM 1117 SG CYS A 154 103.357 120.580 115.564 1.00 0.00 S ATOM 1162 SG CYS A 184 102.525 116.811 117.366 1.00 0.00 S ATOM 20402 SG CYS B1119 63.038 131.166 113.345 1.00 0.00 S ATOM 20424 SG CYS B1122 66.171 128.694 112.348 1.00 0.00 S ATOM 20539 SG CYS B1137 62.043 127.322 113.528 1.00 0.00 S ATOM 20560 SG CYS B1140 65.317 128.308 115.652 1.00 0.00 S ATOM 21535 SG CYS C 88 10.588 127.248 52.370 1.00 0.00 S ATOM 21548 SG CYS C 90 11.666 123.927 54.909 1.00 0.00 S ATOM 21583 SG CYS C 94 9.643 123.490 51.663 1.00 0.00 S ATOM 21605 SG CYS C 97 13.399 124.088 51.386 1.00 0.00 S ATOM 29208 SG CYS I 17 130.635 89.377 62.996 1.00 0.00 S ATOM 29232 SG CYS I 20 127.730 88.786 65.147 1.00 0.00 S ATOM 29393 SG CYS I 39 128.703 91.811 66.272 1.00 0.00 S ATOM 29418 SG CYS I 42 131.132 88.917 66.797 1.00 0.00 S ATOM 29770 SG CYS I 86 114.022 106.936 24.394 1.00 0.00 S ATOM 29794 SG CYS I 89 112.841 104.933 21.484 1.00 0.00 S ATOM 29998 SG CYS I 114 111.111 104.955 24.914 1.00 0.00 S ATOM 30033 SG CYS I 119 115.057 103.571 24.121 1.00 0.00 S ATOM 30143 SG CYS J 7 40.276 122.721 34.835 1.00 0.00 S ATOM 30167 SG CYS J 10 38.429 125.267 33.207 1.00 0.00 S ATOM 30431 SG CYS J 44 42.174 125.023 32.224 1.00 0.00 S ATOM 30437 SG CYS J 45 39.294 123.124 30.629 1.00 0.00 S ATOM 31616 SG CYS L 19 36.136 86.898 60.207 1.00 0.00 S ATOM 31635 SG CYS L 22 33.508 85.778 57.877 1.00 0.00 S ATOM 31752 SG CYS L 36 33.088 84.428 61.180 1.00 0.00 S ATOM 31778 SG CYS L 39 36.763 83.294 58.618 1.00 0.00 S ATOM 32013 SG CYS M 15 29.338 123.746 97.070 1.00 0.00 S ATOM 32160 SG CYS M 34 29.436 121.542 93.642 1.00 0.00 S ATOM 32182 SG CYS M 37 28.238 125.387 93.598 1.00 0.00 S ATOM 38417 SG CYS Q 129 36.550 114.091 127.056 1.00 0.00 S ATOM 38437 SG CYS Q 132 39.763 113.670 124.846 1.00 0.00 S ATOM 38609 SG CYS Q 154 38.164 117.134 124.907 1.00 0.00 S ATOM 38633 SG CYS Q 157 36.423 114.241 123.143 1.00 0.00 S ATOM 44342 SG CYS U 263 87.514 156.413 48.454 1.00 0.00 S ATOM 44361 SG CYS U 266 91.492 157.050 48.400 1.00 0.00 S ATOM 44559 SG CYS U 291 89.751 153.469 48.929 1.00 0.00 S ATOM 44582 SG CYS U 294 89.670 156.177 51.799 1.00 0.00 S Time building chain proxies: 23.60, per 1000 atoms: 0.49 Number of scatterers: 47927 At special positions: 0 Unit cell: (180.78, 209.6, 170.3, 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 11 29.99 S 270 16.00 P 158 15.00 Mg 2 11.99 O 9371 8.00 N 8418 7.00 C 29697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.90 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN Q 501 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 157 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 129 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 132 " pdb=" ZN U 401 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 291 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 266 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 294 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 263 " Number of angles added : 60 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 56 sheets defined 41.3% alpha, 18.9% beta 49 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 15.71 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.537A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.568A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.672A pdb=" N CYS A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 300 through 319 Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.318A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.501A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.630A pdb=" N MET A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.918A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.677A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.808A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.598A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 820 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.760A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.662A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.588A pdb=" N LYS A 940 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 943 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.542A pdb=" N THR A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.690A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1101 removed outlier: 3.585A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 3.553A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.507A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1189 through 1196 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1387 removed outlier: 7.590A pdb=" N ILE A1371 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N GLU A1372 " --> pdb=" O VAL A1368 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1373 " --> pdb=" O LEU A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.969A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.800A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.677A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 removed outlier: 3.644A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.515A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1484 Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.589A pdb=" N CYS B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.706A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 4.627A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 309 removed outlier: 3.660A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 removed outlier: 3.824A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.824A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.868A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.071A pdb=" N THR B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.830A pdb=" N GLU B 600 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.667A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.592A pdb=" N MET B 702 " --> pdb=" O HIS B 699 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.555A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 978 through 994 removed outlier: 3.671A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1019 Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.605A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1107 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.588A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.622A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.573A pdb=" N ILE C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.165A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.716A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.616A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.551A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.693A pdb=" N GLY H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.618A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.504A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.991A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.108A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.892A pdb=" N GLU M 51 " --> pdb=" O ASP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 128 removed outlier: 3.725A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.531A pdb=" N LYS M 149 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.525A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.085A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 264 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.680A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'N' and resid 10 through 33 removed outlier: 4.355A pdb=" N ASP N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 51 Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'N' and resid 312 through 318 removed outlier: 4.212A pdb=" N ASN N 315 " --> pdb=" O GLU N 312 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU N 317 " --> pdb=" O LEU N 314 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP N 318 " --> pdb=" O ASN N 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 3.975A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 29 through 51 Processing helix chain 'P' and resid 153 through 160 removed outlier: 6.264A pdb=" N SER P 158 " --> pdb=" O ALA P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 187 Processing helix chain 'P' and resid 226 through 244 Processing helix chain 'P' and resid 269 through 277 Processing helix chain 'P' and resid 317 through 334 removed outlier: 3.580A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 12 through 25 Processing helix chain 'Q' and resid 27 through 40 removed outlier: 4.305A pdb=" N ALA Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE Q 36 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Q 40 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 53 Processing helix chain 'Q' and resid 55 through 70 Processing helix chain 'Q' and resid 102 through 119 Processing helix chain 'Q' and resid 137 through 144 removed outlier: 4.054A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 188 Proline residue: Q 186 - end of helix Processing helix chain 'Q' and resid 188 through 204 Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 108 through 111 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 151 through 157 removed outlier: 3.890A pdb=" N GLN R 157 " --> pdb=" O ARG R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 174 removed outlier: 4.203A pdb=" N ALA R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 185 removed outlier: 4.630A pdb=" N LYS R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 221 Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 104 through 107 Processing helix chain 'S' and resid 160 through 168 Processing helix chain 'S' and resid 173 through 180 removed outlier: 4.244A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG S 180 " --> pdb=" O ILE S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 5 Processing helix chain 'T' and resid 9 through 15 Processing helix chain 'T' and resid 25 through 33 removed outlier: 3.584A pdb=" N LYS T 33 " --> pdb=" O GLN T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 137 removed outlier: 3.602A pdb=" N LEU T 127 " --> pdb=" O ASN T 123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS T 137 " --> pdb=" O GLU T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 169 Processing helix chain 'T' and resid 179 through 194 removed outlier: 3.606A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 207 Processing helix chain 'T' and resid 209 through 221 Processing helix chain 'U' and resid 138 through 153 Processing helix chain 'U' and resid 156 through 162 removed outlier: 3.740A pdb=" N ALA U 160 " --> pdb=" O ASP U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 181 Processing helix chain 'U' and resid 184 through 199 Processing helix chain 'U' and resid 203 through 212 removed outlier: 4.298A pdb=" N ARG U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 221 Processing helix chain 'U' and resid 232 through 248 Processing helix chain 'U' and resid 292 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 4.088A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.616A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.902A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.118A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.738A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.459A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG H 57 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.658A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.533A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 901 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.547A pdb=" N MET A1309 " --> pdb=" O GLU A1337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1163 through 1165 removed outlier: 4.438A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1298 " --> pdb=" O THR A1164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 4.208A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1321 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.715A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.223A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 205 through 209 removed outlier: 6.561A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.132A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.762A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 926 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N THR B 901 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 5.427A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.687A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD6, first strand: chain 'C' and resid 9 through 14 removed outlier: 5.420A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.748A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.766A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.320A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.596A pdb=" N VAL E 106 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.787A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN G 91 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE7, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE8, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.790A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 24 through 25 Processing sheet with id=AF2, first strand: chain 'N' and resid 363 through 366 removed outlier: 5.560A pdb=" N LYS N 354 " --> pdb=" O TYR N 339 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR N 339 " --> pdb=" O LYS N 354 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY N 356 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS N 337 " --> pdb=" O GLY N 356 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET N 358 " --> pdb=" O VAL N 335 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL N 335 " --> pdb=" O MET N 358 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU N 360 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN N 333 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS O 98 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU O 87 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG O 82 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS O 89 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU O 80 " --> pdb=" O LYS O 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP O 91 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP O 72 " --> pdb=" O PHE O 67 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE O 67 " --> pdb=" O TRP O 72 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE O 74 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR O 65 " --> pdb=" O PHE O 74 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU O 76 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN O 63 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP O 78 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER O 61 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN P 173 " --> pdb=" O ASP P 252 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP P 252 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 363 through 366 removed outlier: 6.390A pdb=" N LYS N 369 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE O 58 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE N 371 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY O 60 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP N 373 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU O 62 " --> pdb=" O ASP N 373 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU N 375 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR O 64 " --> pdb=" O GLU N 375 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN P 173 " --> pdb=" O ASP P 252 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP P 252 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 43 through 44 Processing sheet with id=AF5, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.531A pdb=" N THR Q 151 " --> pdb=" O ASP Q 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 131 through 133 Processing sheet with id=AF7, first strand: chain 'R' and resid 165 through 166 removed outlier: 4.101A pdb=" N GLY R 165 " --> pdb=" O PHE R 202 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 202 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 45 through 49 removed outlier: 6.760A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL T 18 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ALA T 114 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU T 20 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS T 116 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS T 22 " --> pdb=" O CYS T 116 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY T 41 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG T 51 " --> pdb=" O THR T 48 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 45 through 49 removed outlier: 6.760A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP T 8 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY T 108 " --> pdb=" O ASP T 8 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 197 through 198 Processing sheet with id=AG2, first strand: chain 'U' and resid 272 through 274 1999 hydrogen bonds defined for protein. 5493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 254 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 27.06 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 7817 1.30 - 1.45: 13975 1.45 - 1.60: 26628 1.60 - 1.75: 283 1.75 - 1.90: 423 Bond restraints: 49126 Sorted by residual: bond pdb=" CA ASN R 204 " pdb=" C ASN R 204 " ideal model delta sigma weight residual 1.522 1.614 -0.092 1.20e-02 6.94e+03 5.89e+01 bond pdb=" CA VAL A 521 " pdb=" CB VAL A 521 " ideal model delta sigma weight residual 1.537 1.574 -0.038 5.00e-03 4.00e+04 5.63e+01 bond pdb=" N ASN R 204 " pdb=" CA ASN R 204 " ideal model delta sigma weight residual 1.456 1.539 -0.083 1.16e-02 7.43e+03 5.14e+01 bond pdb=" CA CYS A1159 " pdb=" CB CYS A1159 " ideal model delta sigma weight residual 1.528 1.639 -0.110 1.59e-02 3.96e+03 4.83e+01 bond pdb=" C PHE A 482 " pdb=" O PHE A 482 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.21e-02 6.83e+03 4.69e+01 ... (remaining 49121 not shown) Histogram of bond angle deviations from ideal: 57.05 - 73.25: 3 73.25 - 89.46: 5 89.46 - 105.66: 2039 105.66 - 121.87: 53834 121.87 - 138.07: 11129 Bond angle restraints: 67010 Sorted by residual: angle pdb=" N VAL Q 102 " pdb=" CA VAL Q 102 " pdb=" C VAL Q 102 " ideal model delta sigma weight residual 112.43 88.29 24.14 9.20e-01 1.18e+00 6.89e+02 angle pdb=" N LEU J 65 " pdb=" CA LEU J 65 " pdb=" C LEU J 65 " ideal model delta sigma weight residual 113.16 89.71 23.45 1.24e+00 6.50e-01 3.58e+02 angle pdb=" C HIS I 84 " pdb=" N PRO I 85 " pdb=" CD PRO I 85 " ideal model delta sigma weight residual 125.00 57.05 67.95 4.10e+00 5.95e-02 2.75e+02 angle pdb=" N ASP U 231 " pdb=" CA ASP U 231 " pdb=" C ASP U 231 " ideal model delta sigma weight residual 113.50 94.28 19.22 1.23e+00 6.61e-01 2.44e+02 angle pdb=" N SER B 882 " pdb=" CA SER B 882 " pdb=" C SER B 882 " ideal model delta sigma weight residual 111.81 90.04 21.77 1.44e+00 4.82e-01 2.29e+02 ... (remaining 67005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 28461 35.87 - 71.73: 1134 71.73 - 107.60: 80 107.60 - 143.46: 0 143.46 - 179.33: 7 Dihedral angle restraints: 29682 sinusoidal: 13423 harmonic: 16259 Sorted by residual: dihedral pdb=" CA TYR A1308 " pdb=" C TYR A1308 " pdb=" N MET A1309 " pdb=" CA MET A1309 " ideal model delta harmonic sigma weight residual 180.00 105.49 74.51 0 5.00e+00 4.00e-02 2.22e+02 dihedral pdb=" CA ILE N 371 " pdb=" C ILE N 371 " pdb=" N GLY N 372 " pdb=" CA GLY N 372 " ideal model delta harmonic sigma weight residual -180.00 -125.59 -54.41 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ALA Q 125 " pdb=" C ALA Q 125 " pdb=" N SER Q 126 " pdb=" CA SER Q 126 " ideal model delta harmonic sigma weight residual 180.00 -129.47 -50.53 0 5.00e+00 4.00e-02 1.02e+02 ... (remaining 29679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 7247 0.191 - 0.383: 184 0.383 - 0.574: 21 0.574 - 0.766: 3 0.766 - 0.957: 1 Chirality restraints: 7456 Sorted by residual: chirality pdb=" CA LEU M 39 " pdb=" N LEU M 39 " pdb=" C LEU M 39 " pdb=" CB LEU M 39 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" CA LEU R 163 " pdb=" N LEU R 163 " pdb=" C LEU R 163 " pdb=" CB LEU R 163 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA LEU B 880 " pdb=" N LEU B 880 " pdb=" C LEU B 880 " pdb=" CB LEU B 880 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 7453 not shown) Planarity restraints: 8154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 10 " -0.167 5.00e-02 4.00e+02 2.60e-01 1.08e+02 pdb=" N PRO M 11 " 0.445 5.00e-02 4.00e+02 pdb=" CA PRO M 11 " -0.190 5.00e-02 4.00e+02 pdb=" CD PRO M 11 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 84 " 0.204 5.00e-02 4.00e+02 2.58e-01 1.07e+02 pdb=" N PRO I 85 " -0.431 5.00e-02 4.00e+02 pdb=" CA PRO I 85 " 0.196 5.00e-02 4.00e+02 pdb=" CD PRO I 85 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.156 5.00e-02 4.00e+02 2.35e-01 8.86e+01 pdb=" N PRO C 7 " 0.403 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.169 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.078 5.00e-02 4.00e+02 ... (remaining 8151 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 33 1.91 - 2.66: 1520 2.66 - 3.40: 65580 3.40 - 4.15: 114269 4.15 - 4.90: 199488 Nonbonded interactions: 380890 Sorted by model distance: nonbonded pdb=" C VAL A 264 " pdb=" ND2 ASN A 272 " model vdw 1.160 3.350 nonbonded pdb=" CE2 PHE Q 180 " pdb=" OD1 ASP R 213 " model vdw 1.174 3.340 nonbonded pdb=" N VAL A 265 " pdb=" ND2 ASN A 272 " model vdw 1.181 3.200 nonbonded pdb=" OH TYR Q 20 " pdb=" CA PHE R 210 " model vdw 1.239 3.470 nonbonded pdb=" O VAL R 225 " pdb=" N SER R 227 " model vdw 1.273 2.520 ... (remaining 380885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 14.370 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 143.720 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 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 : 0.012 0.141 49126 Z= 0.754 Angle : 1.763 67.954 67010 Z= 1.114 Chirality : 0.079 0.957 7456 Planarity : 0.013 0.260 8154 Dihedral : 17.245 179.329 19154 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 4.18 % Allowed : 8.18 % Favored : 87.64 % Rotamer: Outliers : 3.83 % Allowed : 5.05 % Favored : 91.12 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.20 (0.10), residues: 5525 helix: -0.52 (0.10), residues: 1987 sheet: -0.62 (0.18), residues: 725 loop : -2.46 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.006 TRP C 49 HIS 0.056 0.003 HIS B 287 PHE 0.066 0.004 PHE R 210 TYR 0.104 0.006 TYR R 236 ARG 0.074 0.006 ARG A1160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2241 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2052 time to evaluate : 5.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 354 LEU cc_start: 0.8836 (tp) cc_final: 0.8472 (tp) REVERT: A 461 GLN cc_start: 0.8423 (mt0) cc_final: 0.8138 (mt0) REVERT: A 501 MET cc_start: 0.8428 (mtp) cc_final: 0.8134 (mtp) REVERT: A 516 GLN cc_start: 0.8199 (tt0) cc_final: 0.7893 (tt0) REVERT: A 552 ASP cc_start: 0.7956 (p0) cc_final: 0.7630 (m-30) REVERT: A 680 LEU cc_start: 0.8347 (tp) cc_final: 0.6863 (tp) REVERT: A 691 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: A 781 ILE cc_start: 0.9030 (mm) cc_final: 0.8807 (mt) REVERT: A 819 SER cc_start: 0.8297 (m) cc_final: 0.8080 (m) REVERT: A 849 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6899 (t70) REVERT: A 864 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9093 (tt) REVERT: A 868 MET cc_start: 0.8668 (mmm) cc_final: 0.8303 (mmm) REVERT: A 872 MET cc_start: 0.8543 (ptm) cc_final: 0.8323 (ptt) REVERT: A 874 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8177 (mmtt) REVERT: A 1086 MET cc_start: 0.8845 (mmm) cc_final: 0.8498 (mmm) REVERT: A 1130 ILE cc_start: 0.8900 (mt) cc_final: 0.8510 (mt) REVERT: A 1195 VAL cc_start: 0.6353 (t) cc_final: 0.5731 (t) REVERT: A 1197 TYR cc_start: 0.4332 (p90) cc_final: 0.4089 (p90) REVERT: A 1212 LEU cc_start: 0.6855 (tp) cc_final: 0.6616 (tp) REVERT: A 1257 LEU cc_start: 0.8496 (tp) cc_final: 0.8265 (tp) REVERT: A 1387 SER cc_start: 0.7763 (m) cc_final: 0.7448 (t) REVERT: A 1408 ARG cc_start: 0.7019 (ptt180) cc_final: 0.6724 (ptm-80) REVERT: A 1412 MET cc_start: 0.7517 (ttp) cc_final: 0.7156 (ttt) REVERT: B 48 ASP cc_start: 0.7158 (t0) cc_final: 0.6908 (t0) REVERT: B 93 LEU cc_start: 0.8115 (tp) cc_final: 0.7874 (tp) REVERT: B 129 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (p) REVERT: B 191 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 319 ASN cc_start: 0.5356 (t0) cc_final: 0.4777 (t0) REVERT: B 343 LEU cc_start: 0.8421 (tp) cc_final: 0.8093 (tp) REVERT: B 431 LEU cc_start: 0.8528 (tp) cc_final: 0.8220 (tp) REVERT: B 433 LEU cc_start: 0.8799 (mt) cc_final: 0.8535 (mt) REVERT: B 442 ASP cc_start: 0.5821 (m-30) cc_final: 0.4993 (m-30) REVERT: B 483 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7944 (mtp85) REVERT: B 545 LEU cc_start: 0.7739 (mt) cc_final: 0.7485 (mt) REVERT: B 726 SER cc_start: 0.9325 (m) cc_final: 0.9077 (t) REVERT: B 737 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8630 (pt) REVERT: B 790 GLN cc_start: 0.8380 (mt0) cc_final: 0.8152 (mt0) REVERT: B 791 GLU cc_start: 0.8467 (tp30) cc_final: 0.7870 (mt-10) REVERT: B 793 SER cc_start: 0.9093 (p) cc_final: 0.8267 (m) REVERT: B 854 ILE cc_start: 0.9328 (pt) cc_final: 0.8969 (tt) REVERT: B 906 GLN cc_start: 0.8064 (mt0) cc_final: 0.7673 (mt0) REVERT: B 913 GLN cc_start: 0.7898 (pt0) cc_final: 0.7455 (pt0) REVERT: B 933 ASP cc_start: 0.7352 (m-30) cc_final: 0.6955 (m-30) REVERT: B 1033 THR cc_start: 0.8977 (p) cc_final: 0.8762 (t) REVERT: B 1035 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8132 (ttt-90) REVERT: B 1037 ILE cc_start: 0.9281 (mt) cc_final: 0.9043 (mt) REVERT: B 1054 MET cc_start: 0.8446 (mtm) cc_final: 0.8057 (mtp) REVERT: B 1124 ILE cc_start: 0.7807 (mp) cc_final: 0.7497 (mt) REVERT: C 35 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8365 (ttp80) REVERT: C 44 ILE cc_start: 0.8364 (tt) cc_final: 0.8038 (tt) REVERT: C 134 ASN cc_start: 0.5116 (m-40) cc_final: 0.4896 (m110) REVERT: C 149 LEU cc_start: 0.8066 (tt) cc_final: 0.7809 (tt) REVERT: E 23 ASP cc_start: 0.7162 (m-30) cc_final: 0.6857 (m-30) REVERT: E 144 LEU cc_start: 0.8809 (mt) cc_final: 0.8483 (mt) REVERT: E 193 ILE cc_start: 0.9244 (mp) cc_final: 0.9043 (mp) REVERT: F 121 ASP cc_start: 0.6519 (p0) cc_final: 0.6216 (p0) REVERT: G 68 TYR cc_start: 0.7267 (m-80) cc_final: 0.7058 (m-80) REVERT: G 134 ASP cc_start: 0.4439 (p0) cc_final: 0.4206 (p0) REVERT: G 158 PHE cc_start: 0.0831 (OUTLIER) cc_final: 0.0333 (p90) REVERT: H 30 CYS cc_start: 0.6496 (m) cc_final: 0.6138 (m) REVERT: H 116 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8224 (t) REVERT: H 121 LEU cc_start: 0.8863 (mp) cc_final: 0.8647 (mt) REVERT: H 144 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8370 (mp) REVERT: I 1 MET cc_start: -0.0362 (mtt) cc_final: -0.1283 (mtt) REVERT: I 25 TYR cc_start: 0.5087 (m-80) cc_final: 0.4795 (m-10) REVERT: J 21 TYR cc_start: 0.8019 (t80) cc_final: 0.7775 (t80) REVERT: K 91 ILE cc_start: 0.8021 (mt) cc_final: 0.7692 (mt) REVERT: K 100 LEU cc_start: 0.7654 (tp) cc_final: 0.7025 (tt) REVERT: M 161 SER cc_start: 0.8482 (m) cc_final: 0.7601 (t) REVERT: M 291 LEU cc_start: 0.6539 (tp) cc_final: 0.6310 (tp) REVERT: N 21 VAL cc_start: 0.5207 (t) cc_final: 0.4912 (m) REVERT: Q 62 VAL cc_start: 0.6867 (t) cc_final: 0.6638 (t) REVERT: Q 76 MET cc_start: 0.4348 (OUTLIER) cc_final: 0.3873 (mmt) REVERT: U 140 VAL cc_start: 0.5648 (t) cc_final: 0.4111 (t) REVERT: U 142 LEU cc_start: 0.4806 (mt) cc_final: 0.4355 (mt) REVERT: U 177 TYR cc_start: 0.4727 (t80) cc_final: 0.4460 (t80) REVERT: U 252 LYS cc_start: -0.0919 (OUTLIER) cc_final: -0.1385 (tppt) REVERT: U 262 THR cc_start: 0.1881 (m) cc_final: 0.1192 (m) outliers start: 189 outliers final: 55 residues processed: 2166 average time/residue: 0.6575 time to fit residues: 2226.0108 Evaluate side-chains 1380 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1313 time to evaluate : 5.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1308 TYR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1035 ARG Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 171 LYS Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain U residue 194 ARG Chi-restraints excluded: chain U residue 252 LYS Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 257 GLN Chi-restraints excluded: chain U residue 276 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 477 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 288 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 442 optimal weight: 8.9990 chunk 171 optimal weight: 0.6980 chunk 269 optimal weight: 0.3980 chunk 329 optimal weight: 0.5980 chunk 513 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 152 ASN A 222 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 459 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 620 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 780 ASN A 989 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN A1445 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 141 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 370 HIS B 390 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 260 GLN C 275 ASN D 43 HIS D 141 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 46 GLN F 49 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS K 76 GLN K 89 ASN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 148 GLN M 234 HIS ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 ASN T 144 GLN T 159 HIS T 198 ASN ** U 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 HIS ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 49126 Z= 0.297 Angle : 0.913 27.328 67010 Z= 0.472 Chirality : 0.049 0.412 7456 Planarity : 0.007 0.196 8154 Dihedral : 17.750 179.712 7942 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 1.10 % Allowed : 7.93 % Favored : 90.97 % Rotamer: Outliers : 5.09 % Allowed : 16.61 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.61 % 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: -1.06 (0.11), residues: 5525 helix: 0.55 (0.11), residues: 2032 sheet: -0.30 (0.18), residues: 733 loop : -1.83 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 49 HIS 0.017 0.002 HIS A1417 PHE 0.049 0.003 PHE Q 54 TYR 0.037 0.002 TYR Q 20 ARG 0.018 0.001 ARG U 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1484 time to evaluate : 5.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 236 LEU cc_start: 0.6511 (mt) cc_final: 0.6267 (mt) REVERT: A 258 LEU cc_start: 0.7732 (mt) cc_final: 0.6947 (mp) REVERT: A 272 ASN cc_start: 0.5462 (OUTLIER) cc_final: 0.5156 (p0) REVERT: A 349 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6949 (tpp80) REVERT: A 461 GLN cc_start: 0.8559 (mt0) cc_final: 0.8329 (mt0) REVERT: A 514 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 626 THR cc_start: 0.7541 (p) cc_final: 0.7328 (m) REVERT: A 639 ILE cc_start: 0.8614 (mp) cc_final: 0.8160 (pt) REVERT: A 790 GLN cc_start: 0.7425 (tp40) cc_final: 0.7210 (tp-100) REVERT: A 861 GLN cc_start: 0.7458 (tt0) cc_final: 0.7257 (tt0) REVERT: A 1121 VAL cc_start: 0.8114 (t) cc_final: 0.7861 (t) REVERT: A 1361 ASP cc_start: 0.7843 (t70) cc_final: 0.6962 (t0) REVERT: A 1387 SER cc_start: 0.7899 (m) cc_final: 0.7491 (t) REVERT: A 1389 ASP cc_start: 0.5256 (t0) cc_final: 0.5044 (t0) REVERT: A 1408 ARG cc_start: 0.6557 (ptt180) cc_final: 0.6174 (ptm-80) REVERT: B 108 MET cc_start: 0.7968 (ttm) cc_final: 0.7658 (ttm) REVERT: B 239 MET cc_start: 0.7785 (tpp) cc_final: 0.7485 (tpp) REVERT: B 343 LEU cc_start: 0.8344 (tp) cc_final: 0.8036 (tp) REVERT: B 432 GLU cc_start: 0.5779 (tm-30) cc_final: 0.5438 (tm-30) REVERT: B 508 MET cc_start: 0.8878 (mmt) cc_final: 0.8533 (mmp) REVERT: B 640 ILE cc_start: 0.7350 (mm) cc_final: 0.7145 (mm) REVERT: B 674 MET cc_start: 0.8873 (tpp) cc_final: 0.8657 (tpp) REVERT: B 709 SER cc_start: 0.9187 (m) cc_final: 0.8966 (m) REVERT: B 711 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8788 (tt) REVERT: B 906 GLN cc_start: 0.7967 (mt0) cc_final: 0.7638 (mt0) REVERT: B 913 GLN cc_start: 0.7830 (pt0) cc_final: 0.7562 (pt0) REVERT: B 933 ASP cc_start: 0.7072 (m-30) cc_final: 0.6702 (m-30) REVERT: B 1037 ILE cc_start: 0.9209 (mt) cc_final: 0.8946 (mt) REVERT: B 1124 ILE cc_start: 0.7824 (mp) cc_final: 0.7553 (mt) REVERT: C 44 ILE cc_start: 0.8265 (tt) cc_final: 0.7968 (tt) REVERT: C 149 LEU cc_start: 0.7981 (tt) cc_final: 0.7384 (tt) REVERT: G 29 LYS cc_start: 0.7025 (tppt) cc_final: 0.6581 (tppp) REVERT: G 68 TYR cc_start: 0.7400 (m-80) cc_final: 0.7031 (m-80) REVERT: G 86 ASP cc_start: 0.3136 (t0) cc_final: 0.2373 (p0) REVERT: H 121 LEU cc_start: 0.8791 (mp) cc_final: 0.8550 (mt) REVERT: I 1 MET cc_start: -0.0692 (mtt) cc_final: -0.1316 (mtt) REVERT: I 65 LEU cc_start: 0.5852 (mt) cc_final: 0.5570 (mt) REVERT: M 191 ILE cc_start: 0.7955 (tp) cc_final: 0.7581 (tp) REVERT: M 244 LEU cc_start: 0.6804 (mt) cc_final: 0.6584 (mp) REVERT: P 257 ASN cc_start: 0.3272 (OUTLIER) cc_final: 0.2887 (m-40) REVERT: S 177 MET cc_start: 0.3787 (mpp) cc_final: 0.3474 (mpp) REVERT: T 94 THR cc_start: 0.3599 (p) cc_final: 0.3100 (p) REVERT: U 143 LYS cc_start: 0.5531 (pptt) cc_final: 0.4766 (pptt) REVERT: U 299 LYS cc_start: 0.0272 (OUTLIER) cc_final: -0.0103 (ptmt) outliers start: 251 outliers final: 129 residues processed: 1626 average time/residue: 0.6335 time to fit residues: 1658.6280 Evaluate side-chains 1327 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1192 time to evaluate : 5.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1029 TYR Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 11 PRO Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 257 ASN Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 128 LYS Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 291 CYS Chi-restraints excluded: chain U residue 299 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 427 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 514 optimal weight: 20.0000 chunk 555 optimal weight: 8.9990 chunk 457 optimal weight: 10.0000 chunk 509 optimal weight: 0.1980 chunk 175 optimal weight: 0.8980 chunk 412 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 780 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN A1077 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 486 ASN B 525 ASN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 89 ASN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 ASN ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 257 GLN U 270 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 49126 Z= 0.381 Angle : 0.868 18.613 67010 Z= 0.448 Chirality : 0.048 0.370 7456 Planarity : 0.007 0.183 8154 Dihedral : 17.421 179.824 7840 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.71 % Favored : 90.41 % Rotamer: Outliers : 5.62 % Allowed : 19.40 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.61 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5525 helix: 0.61 (0.11), residues: 2030 sheet: -0.36 (0.18), residues: 773 loop : -1.75 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 49 HIS 0.016 0.002 HIS B 749 PHE 0.055 0.003 PHE E 75 TYR 0.032 0.002 TYR Q 20 ARG 0.023 0.001 ARG U 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1255 time to evaluate : 5.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 461 GLN cc_start: 0.8626 (mt0) cc_final: 0.8377 (mt0) REVERT: A 639 ILE cc_start: 0.8538 (mp) cc_final: 0.8073 (pt) REVERT: A 769 MET cc_start: 0.8509 (mtp) cc_final: 0.8308 (mtp) REVERT: A 861 GLN cc_start: 0.7536 (tt0) cc_final: 0.7271 (tt0) REVERT: A 1408 ARG cc_start: 0.6682 (ptt180) cc_final: 0.6332 (ptm-80) REVERT: B 23 GLN cc_start: 0.7129 (pp30) cc_final: 0.6573 (pp30) REVERT: B 508 MET cc_start: 0.8826 (mmt) cc_final: 0.8614 (mmt) REVERT: B 640 ILE cc_start: 0.7267 (mm) cc_final: 0.6937 (mm) REVERT: B 674 MET cc_start: 0.8919 (tpp) cc_final: 0.8587 (tpp) REVERT: B 711 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8736 (tt) REVERT: B 906 GLN cc_start: 0.7816 (mt0) cc_final: 0.7600 (mt0) REVERT: B 913 GLN cc_start: 0.7772 (pt0) cc_final: 0.7552 (pt0) REVERT: B 933 ASP cc_start: 0.6993 (m-30) cc_final: 0.6623 (m-30) REVERT: B 985 LEU cc_start: 0.8877 (tp) cc_final: 0.8581 (tp) REVERT: B 1101 GLN cc_start: 0.6897 (mt0) cc_final: 0.6665 (mt0) REVERT: B 1124 ILE cc_start: 0.7952 (mp) cc_final: 0.7709 (mt) REVERT: C 44 ILE cc_start: 0.8463 (tt) cc_final: 0.8173 (tt) REVERT: C 149 LEU cc_start: 0.7794 (tt) cc_final: 0.7268 (tt) REVERT: G 29 LYS cc_start: 0.6828 (tppt) cc_final: 0.6405 (tppp) REVERT: G 86 ASP cc_start: 0.2108 (t0) cc_final: 0.1691 (p0) REVERT: H 144 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8519 (mp) REVERT: I 1 MET cc_start: -0.1409 (mtt) cc_final: -0.1614 (mtt) REVERT: I 36 LEU cc_start: 0.5558 (tp) cc_final: 0.5223 (tt) REVERT: L 44 MET cc_start: 0.8442 (mmt) cc_final: 0.8241 (mmt) REVERT: N 359 ASN cc_start: 0.4313 (p0) cc_final: 0.3933 (t0) REVERT: T 124 TYR cc_start: 0.2842 (t80) cc_final: 0.2608 (t80) REVERT: U 240 LEU cc_start: 0.6662 (mt) cc_final: 0.6277 (mt) outliers start: 277 outliers final: 196 residues processed: 1415 average time/residue: 0.6259 time to fit residues: 1440.8680 Evaluate side-chains 1307 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1109 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 11 PRO Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 295 MET Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 128 LYS Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 161 ILE Chi-restraints excluded: chain U residue 248 HIS Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 507 optimal weight: 20.0000 chunk 386 optimal weight: 0.9980 chunk 266 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 515 optimal weight: 30.0000 chunk 546 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 488 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1024 ASN A1101 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN ** N 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 45 ASN ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 229 GLN ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 203 ASN U 239 ASN U 270 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49126 Z= 0.263 Angle : 0.817 18.744 67010 Z= 0.419 Chirality : 0.047 0.343 7456 Planarity : 0.006 0.176 8154 Dihedral : 17.285 179.456 7829 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.75 % Favored : 91.42 % Rotamer: Outliers : 5.05 % Allowed : 21.65 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 5525 helix: 0.64 (0.11), residues: 2014 sheet: -0.45 (0.18), residues: 783 loop : -1.62 (0.12), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 72 HIS 0.018 0.001 HIS A1417 PHE 0.046 0.002 PHE M 93 TYR 0.032 0.002 TYR A 199 ARG 0.011 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1232 time to evaluate : 5.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.5016 (tpp) cc_final: 0.4520 (tpp) REVERT: A 199 TYR cc_start: 0.4481 (m-10) cc_final: 0.3963 (m-10) REVERT: A 272 ASN cc_start: 0.4900 (OUTLIER) cc_final: 0.4607 (t0) REVERT: A 587 THR cc_start: 0.8374 (p) cc_final: 0.7995 (m) REVERT: A 626 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7378 (m) REVERT: A 639 ILE cc_start: 0.8528 (mp) cc_final: 0.7959 (pt) REVERT: A 733 LEU cc_start: 0.7161 (mm) cc_final: 0.6861 (mm) REVERT: A 861 GLN cc_start: 0.7508 (tt0) cc_final: 0.7274 (tt0) REVERT: A 869 GLU cc_start: 0.7288 (pm20) cc_final: 0.7029 (pm20) REVERT: A 1053 ARG cc_start: 0.7263 (mmm-85) cc_final: 0.6978 (mtp-110) REVERT: A 1054 MET cc_start: 0.6953 (tpp) cc_final: 0.6648 (tpp) REVERT: A 1408 ARG cc_start: 0.6463 (ptt180) cc_final: 0.6082 (ptm-80) REVERT: B 371 ARG cc_start: 0.8343 (tpp80) cc_final: 0.8123 (tpp80) REVERT: B 595 ASP cc_start: 0.5512 (OUTLIER) cc_final: 0.4682 (m-30) REVERT: B 786 THR cc_start: 0.8486 (p) cc_final: 0.8136 (t) REVERT: B 906 GLN cc_start: 0.7954 (mt0) cc_final: 0.7671 (mt0) REVERT: B 913 GLN cc_start: 0.7769 (pt0) cc_final: 0.7494 (pt0) REVERT: B 930 GLN cc_start: 0.7862 (pt0) cc_final: 0.7631 (pt0) REVERT: B 933 ASP cc_start: 0.6880 (m-30) cc_final: 0.6603 (m-30) REVERT: C 44 ILE cc_start: 0.8287 (tt) cc_final: 0.8081 (tt) REVERT: C 149 LEU cc_start: 0.7561 (tt) cc_final: 0.7170 (tt) REVERT: E 182 TYR cc_start: 0.7881 (t80) cc_final: 0.7587 (t80) REVERT: G 29 LYS cc_start: 0.6736 (tppt) cc_final: 0.6275 (tppp) REVERT: H 36 LYS cc_start: 0.5310 (pttp) cc_final: 0.4982 (pttm) REVERT: H 144 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8589 (mp) REVERT: I 24 LEU cc_start: 0.5283 (mm) cc_final: 0.4522 (mm) REVERT: I 44 TYR cc_start: 0.6486 (t80) cc_final: 0.6247 (t80) REVERT: K 105 PHE cc_start: 0.7269 (t80) cc_final: 0.7068 (t80) REVERT: U 233 LEU cc_start: 0.5095 (pp) cc_final: 0.4862 (pp) outliers start: 249 outliers final: 172 residues processed: 1371 average time/residue: 0.6533 time to fit residues: 1470.7112 Evaluate side-chains 1313 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1137 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 229 GLN Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 454 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 406 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 chunk 466 optimal weight: 2.9990 chunk 377 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 490 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A 982 ASN A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 197 GLN B 312 GLN B 319 ASN B 390 ASN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1160 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 333 ASN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 49126 Z= 0.249 Angle : 0.808 17.240 67010 Z= 0.413 Chirality : 0.046 0.314 7456 Planarity : 0.006 0.173 8154 Dihedral : 17.198 179.048 7825 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.71 % Favored : 91.55 % Rotamer: Outliers : 4.91 % Allowed : 22.95 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.11), residues: 5525 helix: 0.63 (0.11), residues: 2026 sheet: -0.40 (0.18), residues: 793 loop : -1.56 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 72 HIS 0.016 0.001 HIS B 577 PHE 0.050 0.002 PHE M 118 TYR 0.027 0.002 TYR A 199 ARG 0.010 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1220 time to evaluate : 5.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 VAL cc_start: 0.7807 (m) cc_final: 0.7501 (t) REVERT: A 272 ASN cc_start: 0.5499 (OUTLIER) cc_final: 0.5034 (t0) REVERT: A 587 THR cc_start: 0.8381 (p) cc_final: 0.8053 (m) REVERT: A 639 ILE cc_start: 0.8370 (mp) cc_final: 0.8035 (pt) REVERT: A 861 GLN cc_start: 0.7522 (tt0) cc_final: 0.7257 (tt0) REVERT: A 869 GLU cc_start: 0.7198 (pm20) cc_final: 0.6874 (pm20) REVERT: A 1053 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6954 (mtp-110) REVERT: A 1054 MET cc_start: 0.7013 (tpp) cc_final: 0.6663 (tpp) REVERT: A 1119 LEU cc_start: 0.7374 (tp) cc_final: 0.7161 (tp) REVERT: A 1189 ASP cc_start: 0.4504 (OUTLIER) cc_final: 0.3998 (m-30) REVERT: A 1302 GLU cc_start: 0.4070 (mp0) cc_final: 0.3822 (mp0) REVERT: A 1403 ASP cc_start: 0.8055 (m-30) cc_final: 0.7829 (m-30) REVERT: A 1408 ARG cc_start: 0.6389 (ptt180) cc_final: 0.6041 (ptm-80) REVERT: A 1460 LEU cc_start: 0.8727 (tp) cc_final: 0.8466 (tp) REVERT: B 590 LEU cc_start: 0.7924 (tp) cc_final: 0.7656 (tp) REVERT: B 595 ASP cc_start: 0.5446 (OUTLIER) cc_final: 0.5197 (m-30) REVERT: B 674 MET cc_start: 0.8785 (tpp) cc_final: 0.8552 (tpp) REVERT: B 786 THR cc_start: 0.8428 (p) cc_final: 0.8099 (t) REVERT: B 824 ASP cc_start: 0.4459 (t0) cc_final: 0.4200 (t0) REVERT: B 906 GLN cc_start: 0.7873 (mt0) cc_final: 0.7647 (mt0) REVERT: B 913 GLN cc_start: 0.7760 (pt0) cc_final: 0.7492 (pt0) REVERT: B 933 ASP cc_start: 0.6964 (m-30) cc_final: 0.6550 (m-30) REVERT: C 44 ILE cc_start: 0.8280 (tt) cc_final: 0.8066 (tt) REVERT: C 149 LEU cc_start: 0.7741 (tt) cc_final: 0.7346 (tt) REVERT: C 254 LYS cc_start: 0.6643 (pttm) cc_final: 0.6234 (pttm) REVERT: E 182 TYR cc_start: 0.8031 (t80) cc_final: 0.7760 (t80) REVERT: G 29 LYS cc_start: 0.6572 (tppt) cc_final: 0.6330 (tppp) REVERT: G 117 MET cc_start: 0.2433 (tpp) cc_final: 0.2084 (tpp) REVERT: G 164 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.5048 (mmt) REVERT: H 95 LYS cc_start: 0.7578 (ptpt) cc_final: 0.7241 (ptpt) REVERT: M 173 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7543 (m) REVERT: M 224 LEU cc_start: 0.6991 (mt) cc_final: 0.6762 (mt) REVERT: U 228 MET cc_start: 0.7044 (tmm) cc_final: 0.6743 (tmm) outliers start: 242 outliers final: 178 residues processed: 1347 average time/residue: 0.6133 time to fit residues: 1341.2116 Evaluate side-chains 1309 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1126 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 102 GLN Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 215 SER Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 183 optimal weight: 1.9990 chunk 491 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 320 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 546 optimal weight: 3.9990 chunk 453 optimal weight: 8.9990 chunk 253 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS A1420 ASN A1422 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 537 GLN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 35 GLN E 64 HIS E 116 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 229 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 49126 Z= 0.271 Angle : 0.819 16.821 67010 Z= 0.418 Chirality : 0.046 0.310 7456 Planarity : 0.006 0.163 8154 Dihedral : 17.167 178.809 7825 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.84 % Favored : 91.42 % Rotamer: Outliers : 5.11 % Allowed : 23.68 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5525 helix: 0.65 (0.11), residues: 2029 sheet: -0.38 (0.18), residues: 797 loop : -1.56 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 72 HIS 0.019 0.001 HIS B 577 PHE 0.041 0.002 PHE M 118 TYR 0.052 0.002 TYR C 3 ARG 0.011 0.001 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1198 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.4924 (tpp) cc_final: 0.4520 (tpp) REVERT: A 226 LYS cc_start: 0.5886 (mttm) cc_final: 0.4750 (mtmm) REVERT: A 272 ASN cc_start: 0.5699 (OUTLIER) cc_final: 0.5237 (t0) REVERT: A 587 THR cc_start: 0.8463 (p) cc_final: 0.8040 (m) REVERT: A 639 ILE cc_start: 0.8343 (mp) cc_final: 0.7993 (pt) REVERT: A 861 GLN cc_start: 0.7532 (tt0) cc_final: 0.7256 (tt0) REVERT: A 869 GLU cc_start: 0.7212 (pm20) cc_final: 0.6925 (pm20) REVERT: A 1054 MET cc_start: 0.7058 (tpp) cc_final: 0.6818 (tpp) REVERT: A 1408 ARG cc_start: 0.6404 (ptt180) cc_final: 0.6031 (ptm-80) REVERT: B 89 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: B 786 THR cc_start: 0.8444 (p) cc_final: 0.8145 (t) REVERT: B 913 GLN cc_start: 0.7816 (pt0) cc_final: 0.7569 (pt0) REVERT: B 933 ASP cc_start: 0.6814 (m-30) cc_final: 0.6405 (m-30) REVERT: B 1072 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6362 (mmm-85) REVERT: C 44 ILE cc_start: 0.8300 (tt) cc_final: 0.8098 (tt) REVERT: C 149 LEU cc_start: 0.7738 (tt) cc_final: 0.7358 (tt) REVERT: C 254 LYS cc_start: 0.6809 (pttm) cc_final: 0.6223 (pttm) REVERT: E 66 ASP cc_start: 0.5608 (t70) cc_final: 0.5319 (t70) REVERT: E 182 TYR cc_start: 0.8045 (t80) cc_final: 0.7724 (t80) REVERT: G 29 LYS cc_start: 0.6726 (tppt) cc_final: 0.6320 (tppp) REVERT: I 36 LEU cc_start: 0.5762 (tp) cc_final: 0.5429 (tt) REVERT: M 83 MET cc_start: 0.5449 (mpp) cc_final: 0.5023 (mpp) REVERT: M 173 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7619 (m) REVERT: P 279 GLN cc_start: 0.5472 (pm20) cc_final: 0.5201 (pm20) REVERT: U 207 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5797 (ptm-80) outliers start: 252 outliers final: 205 residues processed: 1329 average time/residue: 0.6134 time to fit residues: 1324.4010 Evaluate side-chains 1315 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1105 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1222 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 343 HIS Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 215 SER Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 527 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 399 optimal weight: 3.9990 chunk 309 optimal weight: 0.0070 chunk 460 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 544 optimal weight: 6.9990 chunk 340 optimal weight: 0.0050 chunk 332 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 overall best weight: 0.8814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN B 245 GLN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 ASN S 141 HIS U 197 ASN U 270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 49126 Z= 0.273 Angle : 0.830 16.463 67010 Z= 0.422 Chirality : 0.046 0.308 7456 Planarity : 0.006 0.159 8154 Dihedral : 17.150 178.565 7822 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.07 % Favored : 91.26 % Rotamer: Outliers : 5.03 % Allowed : 24.86 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5525 helix: 0.64 (0.12), residues: 2021 sheet: -0.36 (0.18), residues: 791 loop : -1.56 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1192 HIS 0.021 0.001 HIS B 577 PHE 0.065 0.002 PHE S 138 TYR 0.041 0.002 TYR C 3 ARG 0.011 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1189 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.4627 (pt) REVERT: A 272 ASN cc_start: 0.5873 (OUTLIER) cc_final: 0.5395 (t0) REVERT: A 587 THR cc_start: 0.8407 (p) cc_final: 0.8019 (m) REVERT: A 639 ILE cc_start: 0.8263 (mp) cc_final: 0.7961 (pt) REVERT: A 861 GLN cc_start: 0.7565 (tt0) cc_final: 0.7302 (tt0) REVERT: A 869 GLU cc_start: 0.7225 (pm20) cc_final: 0.6868 (pm20) REVERT: A 1054 MET cc_start: 0.7034 (tpp) cc_final: 0.6810 (tpp) REVERT: A 1199 MET cc_start: 0.4408 (mpp) cc_final: 0.4122 (mpp) REVERT: A 1408 ARG cc_start: 0.6326 (ptt180) cc_final: 0.5991 (ptm-80) REVERT: B 298 MET cc_start: 0.5099 (mpp) cc_final: 0.4291 (mpp) REVERT: B 786 THR cc_start: 0.8456 (p) cc_final: 0.8093 (t) REVERT: B 816 GLU cc_start: 0.7212 (tp30) cc_final: 0.6875 (tp30) REVERT: B 913 GLN cc_start: 0.7790 (pt0) cc_final: 0.7563 (pt0) REVERT: B 933 ASP cc_start: 0.6846 (m-30) cc_final: 0.6505 (m-30) REVERT: B 1054 MET cc_start: 0.7692 (mtt) cc_final: 0.7482 (mpp) REVERT: C 44 ILE cc_start: 0.8331 (tt) cc_final: 0.8111 (tt) REVERT: C 149 LEU cc_start: 0.7806 (tt) cc_final: 0.7383 (tt) REVERT: E 182 TYR cc_start: 0.8051 (t80) cc_final: 0.7727 (t80) REVERT: F 84 GLU cc_start: 0.6658 (mp0) cc_final: 0.6375 (mp0) REVERT: G 31 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.5032 (m-10) REVERT: I 36 LEU cc_start: 0.5911 (tp) cc_final: 0.5554 (tt) REVERT: M 83 MET cc_start: 0.5434 (mpp) cc_final: 0.5136 (mpp) REVERT: M 173 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7777 (m) REVERT: O 54 ASN cc_start: 0.1461 (p0) cc_final: 0.1222 (p0) REVERT: Q 67 LYS cc_start: 0.4348 (mmtt) cc_final: 0.3678 (mmtt) REVERT: U 177 TYR cc_start: 0.3314 (t80) cc_final: 0.3098 (t80) REVERT: U 207 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5867 (ptm-80) outliers start: 248 outliers final: 210 residues processed: 1315 average time/residue: 0.6267 time to fit residues: 1343.9943 Evaluate side-chains 1321 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1106 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 315 ASN Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 349 TRP Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 261 SER Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain Q residue 187 ILE Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 141 HIS Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 165 TYR Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 336 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 325 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 346 optimal weight: 0.6980 chunk 371 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 428 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 49126 Z= 0.296 Angle : 0.851 16.435 67010 Z= 0.434 Chirality : 0.047 0.425 7456 Planarity : 0.006 0.155 8154 Dihedral : 17.157 178.426 7820 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.34 % Favored : 91.06 % Rotamer: Outliers : 5.17 % Allowed : 25.93 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5525 helix: 0.58 (0.12), residues: 2023 sheet: -0.42 (0.18), residues: 805 loop : -1.61 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1192 HIS 0.012 0.001 HIS A 313 PHE 0.046 0.002 PHE N 29 TYR 0.038 0.002 TYR C 3 ARG 0.017 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1163 time to evaluate : 5.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASN cc_start: 0.5438 (OUTLIER) cc_final: 0.4999 (t0) REVERT: A 587 THR cc_start: 0.8463 (p) cc_final: 0.8070 (m) REVERT: A 639 ILE cc_start: 0.8310 (mp) cc_final: 0.7836 (pt) REVERT: A 861 GLN cc_start: 0.7551 (tt0) cc_final: 0.7323 (tt0) REVERT: A 1054 MET cc_start: 0.7046 (tpp) cc_final: 0.6761 (tpp) REVERT: A 1168 LYS cc_start: 0.6272 (tptt) cc_final: 0.5899 (tptp) REVERT: A 1408 ARG cc_start: 0.6354 (ptt180) cc_final: 0.5945 (ptm-80) REVERT: A 1412 MET cc_start: 0.7905 (tmm) cc_final: 0.7674 (tmm) REVERT: B 48 ASP cc_start: 0.7100 (m-30) cc_final: 0.6895 (m-30) REVERT: B 529 MET cc_start: 0.7938 (tpp) cc_final: 0.7698 (tpp) REVERT: B 786 THR cc_start: 0.8471 (p) cc_final: 0.8122 (t) REVERT: B 816 GLU cc_start: 0.7222 (tp30) cc_final: 0.6852 (tp30) REVERT: B 913 GLN cc_start: 0.7928 (pt0) cc_final: 0.7609 (pt0) REVERT: B 933 ASP cc_start: 0.6797 (m-30) cc_final: 0.6355 (m-30) REVERT: B 1072 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6487 (mmm-85) REVERT: C 44 ILE cc_start: 0.8368 (tt) cc_final: 0.8143 (tt) REVERT: C 149 LEU cc_start: 0.7798 (tt) cc_final: 0.7383 (tt) REVERT: C 254 LYS cc_start: 0.7152 (pttm) cc_final: 0.6846 (pttm) REVERT: E 13 ILE cc_start: 0.8170 (pt) cc_final: 0.7899 (mt) REVERT: E 182 TYR cc_start: 0.8079 (t80) cc_final: 0.7711 (t80) REVERT: G 31 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.5031 (m-10) REVERT: I 36 LEU cc_start: 0.5993 (tp) cc_final: 0.5687 (tt) REVERT: M 83 MET cc_start: 0.5361 (mpp) cc_final: 0.5110 (mpp) REVERT: M 86 LYS cc_start: 0.5500 (tptt) cc_final: 0.5290 (tptp) REVERT: N 51 MET cc_start: 0.4464 (mmm) cc_final: 0.4223 (mmm) REVERT: O 54 ASN cc_start: 0.1473 (p0) cc_final: 0.1257 (p0) REVERT: Q 67 LYS cc_start: 0.4550 (mmtt) cc_final: 0.4169 (mmtt) REVERT: U 177 TYR cc_start: 0.3282 (t80) cc_final: 0.2896 (t80) REVERT: U 207 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5992 (ptm-80) outliers start: 255 outliers final: 211 residues processed: 1291 average time/residue: 0.6099 time to fit residues: 1284.3621 Evaluate side-chains 1315 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1100 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 919 LYS Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain Q residue 187 ILE Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 141 HIS Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 165 TYR Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 495 optimal weight: 8.9990 chunk 521 optimal weight: 10.0000 chunk 475 optimal weight: 8.9990 chunk 507 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 221 optimal weight: 0.0870 chunk 398 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 458 optimal weight: 0.2980 chunk 479 optimal weight: 1.9990 chunk 505 optimal weight: 8.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 222 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 387 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A1024 ASN A1190 GLN ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS H 46 GLN H 126 GLN I 56 ASN I 84 HIS ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 49126 Z= 0.387 Angle : 0.912 29.915 67010 Z= 0.461 Chirality : 0.048 0.388 7456 Planarity : 0.006 0.206 8154 Dihedral : 17.194 178.704 7820 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.78 % Favored : 90.59 % Rotamer: Outliers : 4.64 % Allowed : 27.09 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -1.10 (0.11), residues: 5525 helix: 0.43 (0.12), residues: 2021 sheet: -0.57 (0.18), residues: 801 loop : -1.70 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP T 233 HIS 0.020 0.002 HIS R 89 PHE 0.055 0.003 PHE M 118 TYR 0.035 0.002 TYR C 3 ARG 0.015 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1117 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 THR cc_start: 0.8491 (p) cc_final: 0.7998 (m) REVERT: A 639 ILE cc_start: 0.8431 (mp) cc_final: 0.7739 (pt) REVERT: A 1054 MET cc_start: 0.7040 (tpp) cc_final: 0.6764 (tpp) REVERT: A 1408 ARG cc_start: 0.6551 (ptt180) cc_final: 0.6170 (ptm-80) REVERT: A 1412 MET cc_start: 0.7890 (tmm) cc_final: 0.7616 (tmm) REVERT: B 48 ASP cc_start: 0.7195 (m-30) cc_final: 0.6991 (m-30) REVERT: B 109 MET cc_start: 0.7675 (mmm) cc_final: 0.7434 (mmm) REVERT: B 432 GLU cc_start: 0.6576 (tm-30) cc_final: 0.5930 (tm-30) REVERT: B 529 MET cc_start: 0.8108 (tpp) cc_final: 0.7758 (tpp) REVERT: B 816 GLU cc_start: 0.7287 (tp30) cc_final: 0.6936 (tp30) REVERT: B 913 GLN cc_start: 0.7833 (pt0) cc_final: 0.7561 (pt0) REVERT: B 933 ASP cc_start: 0.6899 (m-30) cc_final: 0.6503 (m-30) REVERT: B 1151 MET cc_start: 0.7823 (ptm) cc_final: 0.7587 (ptm) REVERT: C 149 LEU cc_start: 0.7865 (tt) cc_final: 0.7434 (tt) REVERT: C 254 LYS cc_start: 0.7476 (pttm) cc_final: 0.6731 (pttm) REVERT: E 13 ILE cc_start: 0.8266 (pt) cc_final: 0.7958 (mt) REVERT: E 182 TYR cc_start: 0.8110 (t80) cc_final: 0.7738 (t80) REVERT: G 31 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5201 (m-10) REVERT: H 27 ARG cc_start: 0.7763 (ttm170) cc_final: 0.7453 (ttt90) REVERT: M 83 MET cc_start: 0.5391 (mpp) cc_final: 0.5134 (mpp) REVERT: O 54 ASN cc_start: 0.1645 (p0) cc_final: 0.1426 (p0) REVERT: S 138 PHE cc_start: 0.2754 (OUTLIER) cc_final: 0.2505 (p90) REVERT: U 207 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6220 (ptm-80) outliers start: 229 outliers final: 193 residues processed: 1242 average time/residue: 0.6108 time to fit residues: 1235.7346 Evaluate side-chains 1265 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1069 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1325 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 194 CYS Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain Q residue 187 ILE Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 138 PHE Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 165 TYR Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 333 optimal weight: 7.9990 chunk 536 optimal weight: 0.9980 chunk 327 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 373 optimal weight: 0.5980 chunk 562 optimal weight: 6.9990 chunk 518 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 346 optimal weight: 0.2980 chunk 274 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 49126 Z= 0.257 Angle : 0.893 18.606 67010 Z= 0.452 Chirality : 0.047 0.306 7456 Planarity : 0.006 0.112 8154 Dihedral : 17.145 177.759 7811 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.11 % Favored : 91.28 % Rotamer: Outliers : 3.59 % Allowed : 28.41 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.11), residues: 5525 helix: 0.43 (0.12), residues: 2015 sheet: -0.64 (0.17), residues: 856 loop : -1.62 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP O 72 HIS 0.043 0.002 HIS B 370 PHE 0.055 0.002 PHE N 29 TYR 0.033 0.002 TYR E 8 ARG 0.014 0.001 ARG L 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1155 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 THR cc_start: 0.8408 (p) cc_final: 0.8001 (m) REVERT: A 639 ILE cc_start: 0.8341 (mp) cc_final: 0.7721 (pt) REVERT: A 1054 MET cc_start: 0.7110 (tpp) cc_final: 0.6908 (tpp) REVERT: A 1361 ASP cc_start: 0.7080 (t0) cc_final: 0.6731 (t0) REVERT: A 1408 ARG cc_start: 0.6304 (ptt180) cc_final: 0.5939 (ptm-80) REVERT: B 48 ASP cc_start: 0.7004 (m-30) cc_final: 0.6780 (m-30) REVERT: B 432 GLU cc_start: 0.6635 (tm-30) cc_final: 0.5824 (tm-30) REVERT: B 529 MET cc_start: 0.8094 (tpp) cc_final: 0.7757 (tpp) REVERT: B 816 GLU cc_start: 0.7237 (tp30) cc_final: 0.6832 (tp30) REVERT: B 913 GLN cc_start: 0.7860 (pt0) cc_final: 0.7638 (pt0) REVERT: B 933 ASP cc_start: 0.7007 (m-30) cc_final: 0.6679 (m-30) REVERT: B 996 ILE cc_start: 0.8466 (mm) cc_final: 0.8201 (mt) REVERT: B 1054 MET cc_start: 0.7734 (mtt) cc_final: 0.7459 (mpp) REVERT: C 254 LYS cc_start: 0.6933 (pttm) cc_final: 0.6647 (pttm) REVERT: E 182 TYR cc_start: 0.8072 (t80) cc_final: 0.7744 (t80) REVERT: G 31 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.5027 (m-10) REVERT: G 68 TYR cc_start: 0.7575 (m-80) cc_final: 0.7344 (m-80) REVERT: H 27 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7411 (ttt90) REVERT: M 83 MET cc_start: 0.5391 (mpp) cc_final: 0.5167 (mpp) REVERT: O 76 LEU cc_start: 0.4299 (mm) cc_final: 0.4023 (mm) REVERT: Q 110 MET cc_start: 0.2781 (mmm) cc_final: 0.2481 (mmm) REVERT: S 138 PHE cc_start: 0.2825 (OUTLIER) cc_final: 0.2534 (p90) REVERT: T 186 MET cc_start: 0.3767 (ppp) cc_final: 0.3508 (ppp) REVERT: U 207 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6016 (ptm-80) outliers start: 177 outliers final: 156 residues processed: 1244 average time/residue: 0.6302 time to fit residues: 1283.3266 Evaluate side-chains 1264 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1105 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 845 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 151 THR Chi-restraints excluded: chain Q residue 177 LEU Chi-restraints excluded: chain Q residue 187 ILE Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 138 PHE Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain T residue 148 VAL Chi-restraints excluded: chain T residue 154 LYS Chi-restraints excluded: chain T residue 161 TYR Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 165 TYR Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 270 ASN Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain U residue 274 THR Chi-restraints excluded: chain U residue 276 VAL Chi-restraints excluded: chain U residue 291 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 356 optimal weight: 6.9990 chunk 477 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 413 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 448 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 460 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A1024 ASN ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 722 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124867 restraints weight = 92237.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122470 restraints weight = 91236.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123516 restraints weight = 91749.743| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 49126 Z= 0.388 Angle : 0.931 20.784 67010 Z= 0.472 Chirality : 0.049 0.510 7456 Planarity : 0.006 0.109 8154 Dihedral : 17.183 178.225 7811 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.01 % Favored : 90.41 % Rotamer: Outliers : 3.71 % Allowed : 28.65 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5525 helix: 0.31 (0.12), residues: 2012 sheet: -0.69 (0.17), residues: 844 loop : -1.73 (0.12), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP O 72 HIS 0.019 0.002 HIS B 577 PHE 0.061 0.003 PHE N 29 TYR 0.033 0.002 TYR C 3 ARG 0.015 0.001 ARG G 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18964.22 seconds wall clock time: 335 minutes 44.08 seconds (20144.08 seconds total)